March 28 2002

NIH Proteomics Workshop

Bethesda MD

Lai-Su Yeh PhD

Protein Scientist National Biomedical Research Foundation

Demo Demo Protein Information ResourceProtein Information Resource

2

Database DemoDatabase DemoNREF Database httppirgeorgetownedupirwwwsearchpirnrefshtml

iProClass Database httppirgeorgetowneduiproclasshtml iProClass Sequence (A58910) Motif (PCM00487)

PIR-PSD Database httppirgeorgetowneducgi-binpirwwwnbrfgetampuid=A58910 PIR Entry (A58910)

Other Molecular Databases Function KEGG Enzyme (EC 111205) KEGG Pathway (

MAP00230) BRENDA (EC 111205) Structure PDB (1AK5) SCOP (1003001006002002) CATH

(1AK5) Family Pfam (PF00478) BLOCKS (BL00487) PROSITE

(PS00487)

2

Database DemoDatabase DemoNREF Database httppirgeorgetownedupirwwwsearchpirnrefshtml

iProClass Database httppirgeorgetowneduiproclasshtml iProClass Sequence (A58910) Motif (PCM00487)

PIR-PSD Database httppirgeorgetowneducgi-binpirwwwnbrfgetampuid=A58910 PIR Entry (A58910)

Other Molecular Databases Function KEGG Enzyme (EC 111205) KEGG Pathway (

MAP00230) BRENDA (EC 111205) Structure PDB (1AK5) SCOP (1003001006002002) CATH

(1AK5) Family Pfam (PF00478) BLOCKS (BL00487) PROSITE

(PS00487)

3

PIR Web Site PIR Web Site (httppirgeorgetownedu)(httppirgeorgetownedu)

4

Text Search Result with Text Search Result with NULLNOT NULLNULLNOT NULL

5

Peptide Search ResultsPeptide Search Results

6

PIR-NREF Search Result (I)PIR-NREF Search Result (I)Test Sequence ftpnbrfageorgetownedupirmisctestseq

7

PIR-NREF Search Result (II)PIR-NREF Search Result (II)

9

PIR Pattern SearchPIR Pattern Search

10

PIR Pattern Search Result (I)PIR Pattern Search Result (I)httppirgeorgetownedupirwwwsearchpatmatchhtml

Pattern Match Sequence vs PROSITE

11

PIR Pattern Search Result (II)PIR Pattern Search Result (II)bullSearch a query pattern against a sequence database

12

PIR Domain Display PIR Domain Display

13

PIR-NREF Database PIR-NREF Database (httppirgeorgetownedupirwwwsearchpirnrefshtml)(httppirgeorgetownedupirwwwsearchpirnrefshtml)

search

14

PIR-NREF ReportPIR-NREF Report

15

PIR-iProClass DatabasePIR-iProClass Database

16

iProClass Sequence ReportiProClass Sequence Report

17

PDB Structure of Molecule Inosine-PDB Structure of Molecule Inosine-5-Monophosphate Dehydrogenase5-Monophosphate Dehydrogenase

18

Related Sequences Related Sequences

19

Protein Family ClassificationProtein Family Classification

Superfamily Domain and Motif ClassificationSuperfamily Concept End-to-End Similarity amp Same Overall Domain Architecture

Significance Improve Sensitivity of Protein Identification Provide Complete Clustering for Database Organization Detect and Correct Genome Annotation Errors Systematically Drive Other Annotations Stimulate Evolution Genomics and Proteomics Research

Discovery of New Knowledge by Using Information Embedded within

Families of Homologous Sequences and Their Structures

20

Protein FamilySuperfamily DefinitionsProtein FamilySuperfamily Definitions

Family A Set of Protein Sequences That Share a Common

Evolutionary Ancestor with End-to-End Sequence Similarity (No Major Discrepancy by Standard Multiple Alignment Methods)

Have the Same Domain Architecture (Except Incomplete or Alternately Spliced)

Overall Sequence Identity gt=45

Superfamily A Set of Protein Families That Share a Common Evolutionary

Ancestor From End-to-end Have the Same Domain Architecture Overall Sequence Identity gt=20

21

Protein Domain DefinitionProtein Domain Definition

Homology Domain A Recognizable Region of Similarity Have a Common Ancestry Found in Diverse Protein Sequences (in gt= 2 Superfamilies)

A Sequence Can Belong to Only One Protein Family and Superfamily but May Contain More Than One Domains

22

Superfamily-Domain-Motif RelationshipSuperfamily-Domain-Motif Relationship

23

iProClass Superfamily ListiProClass Superfamily ListAll Superfamilies Containing PF00001

Superfamily-Domain Relationship ~6000 SFs have gt=1 DomainsSuperfamily for Domain Architecture

24

iProClass Superfamily ReportiProClass Superfamily Report

25

Alignment and Tree ViewAlignment and Tree View

26

PIR-Protein Sequence DatabasePIR-Protein Sequence Database

27

PIR-PSD EntryPIR-PSD Entry

28

BLASTFASTA SearchBLASTFASTA Search

29

PIR FASTA Search ResultPIR FASTA Search Result

30

PIR Searches and AligmentPIR Searches and Aligment BLAST Search

Multiple Alignment amp Tree View

31

PIR Hidden Markov ModelPIR Hidden Markov Modelhttppirgeorgetownedupirwwwsearchpirhmmhtml

HMM Model Building amp Sequence Search

One Protein Against All HMMs

All Proteins Against One HMM

33

Bibliography SubmissionBibliography Submission

View Bibliography Information

View Protein Entry

Submit Citation with Optional Categorization

S1

34

Bibliography Information Display (I)Bibliography Information Display (I)

From PIR-NREF

From Other Curated Database (eg SGD)

35

Bibliography Information Display (II)Bibliography Information Display (II)

From User Submission

From Computer-Mapping (eg Gene Symbol)

36

Oracle DemoOracle DemoJava Web Interface for Oracle Database Search (httppirgeorgetowneduiproclasshtml)

WebDB Interface to Oracle (WebDB) TablesViewsObjects FunctionsProceduresPackages

37

Proteomic BioinformaticsProteomic Bioinformatics

Large-Scale Analysis of Proteomic Data Homology Search for Pathways

• Database Demo
• PIR Web Site (httppirgeorgetownedu)
• Text Search Result with NULLNOT NULL
• Peptide Search Results
• PIR-NREF Search Result (I)
• PIR-NREF Search Result (II)
• PIR Pattern Search
• PIR Pattern Search Result (I)
• PIR Pattern Search Result (II)
• PIR Domain Display
• PIR-NREF Database (httppirgeorgetownedupirwwwsearchpirnrefshtml)
• PIR-NREF Report
• PIR-iProClass Database
• iProClass Sequence Report
• PDB Structure of Molecule Inosine-5-Monophosphate Dehydrogenase
• Related Sequences
• Protein Family Classification
• Protein FamilySuperfamily Definitions
• Protein Domain Definition
• Superfamily-Domain-Motif Relationship
• iProClass Superfamily List
• iProClass Superfamily Report
• Alignment and Tree View
• PIR-Protein Sequence Database
• PIR-PSD Entry
• BLASTFASTA Search
• PIR FASTA Search Result
• PIR Searches and Aligment
• PIR Hidden Markov Model
• Bibliography Submission
• Bibliography Information Display (I)
• Bibliography Information Display (II)
• Oracle Demo
• Proteomic Bioinformatics

4

Text Search Result with Text Search Result with NULLNOT NULLNULLNOT NULL

5

Peptide Search ResultsPeptide Search Results

6

PIR-NREF Search Result (I)PIR-NREF Search Result (I)Test Sequence ftpnbrfageorgetownedupirmisctestseq

7

PIR-NREF Search Result (II)PIR-NREF Search Result (II)

9

PIR Pattern SearchPIR Pattern Search

10

PIR Pattern Search Result (I)PIR Pattern Search Result (I)httppirgeorgetownedupirwwwsearchpatmatchhtml

Pattern Match Sequence vs PROSITE

11

PIR Pattern Search Result (II)PIR Pattern Search Result (II)bullSearch a query pattern against a sequence database

12

PIR Domain Display PIR Domain Display

13

PIR-NREF Database PIR-NREF Database (httppirgeorgetownedupirwwwsearchpirnrefshtml)(httppirgeorgetownedupirwwwsearchpirnrefshtml)

search

14

PIR-NREF ReportPIR-NREF Report

15

PIR-iProClass DatabasePIR-iProClass Database

16

iProClass Sequence ReportiProClass Sequence Report

17

PDB Structure of Molecule Inosine-PDB Structure of Molecule Inosine-5-Monophosphate Dehydrogenase5-Monophosphate Dehydrogenase

18

Related Sequences Related Sequences

19

Protein Family ClassificationProtein Family Classification

Superfamily Domain and Motif ClassificationSuperfamily Concept End-to-End Similarity amp Same Overall Domain Architecture

Significance Improve Sensitivity of Protein Identification Provide Complete Clustering for Database Organization Detect and Correct Genome Annotation Errors Systematically Drive Other Annotations Stimulate Evolution Genomics and Proteomics Research

Discovery of New Knowledge by Using Information Embedded within

Families of Homologous Sequences and Their Structures

20

Protein FamilySuperfamily DefinitionsProtein FamilySuperfamily Definitions

Family A Set of Protein Sequences That Share a Common

Evolutionary Ancestor with End-to-End Sequence Similarity (No Major Discrepancy by Standard Multiple Alignment Methods)

Have the Same Domain Architecture (Except Incomplete or Alternately Spliced)

Overall Sequence Identity gt=45

Superfamily A Set of Protein Families That Share a Common Evolutionary

Ancestor From End-to-end Have the Same Domain Architecture Overall Sequence Identity gt=20

21

Protein Domain DefinitionProtein Domain Definition

Homology Domain A Recognizable Region of Similarity Have a Common Ancestry Found in Diverse Protein Sequences (in gt= 2 Superfamilies)

A Sequence Can Belong to Only One Protein Family and Superfamily but May Contain More Than One Domains

22

Superfamily-Domain-Motif RelationshipSuperfamily-Domain-Motif Relationship

23

iProClass Superfamily ListiProClass Superfamily ListAll Superfamilies Containing PF00001

Superfamily-Domain Relationship ~6000 SFs have gt=1 DomainsSuperfamily for Domain Architecture

24

iProClass Superfamily ReportiProClass Superfamily Report

25

Alignment and Tree ViewAlignment and Tree View

26

PIR-Protein Sequence DatabasePIR-Protein Sequence Database

27

PIR-PSD EntryPIR-PSD Entry

28

BLASTFASTA SearchBLASTFASTA Search

29

PIR FASTA Search ResultPIR FASTA Search Result

30

PIR Searches and AligmentPIR Searches and Aligment BLAST Search

Multiple Alignment amp Tree View

31

PIR Hidden Markov ModelPIR Hidden Markov Modelhttppirgeorgetownedupirwwwsearchpirhmmhtml

HMM Model Building amp Sequence Search

One Protein Against All HMMs

All Proteins Against One HMM

33

Bibliography SubmissionBibliography Submission

View Bibliography Information

View Protein Entry

Submit Citation with Optional Categorization

S1

34

Bibliography Information Display (I)Bibliography Information Display (I)

From PIR-NREF

From Other Curated Database (eg SGD)

35

Bibliography Information Display (II)Bibliography Information Display (II)

From User Submission

From Computer-Mapping (eg Gene Symbol)

36

Oracle DemoOracle DemoJava Web Interface for Oracle Database Search (httppirgeorgetowneduiproclasshtml)

WebDB Interface to Oracle (WebDB) TablesViewsObjects FunctionsProceduresPackages

37

Proteomic BioinformaticsProteomic Bioinformatics

Large-Scale Analysis of Proteomic Data Homology Search for Pathways

• Database Demo
• PIR Web Site (httppirgeorgetownedu)
• Text Search Result with NULLNOT NULL
• Peptide Search Results
• PIR-NREF Search Result (I)
• PIR-NREF Search Result (II)
• PIR Pattern Search
• PIR Pattern Search Result (I)
• PIR Pattern Search Result (II)
• PIR Domain Display
• PIR-NREF Database (httppirgeorgetownedupirwwwsearchpirnrefshtml)
• PIR-NREF Report
• PIR-iProClass Database
• iProClass Sequence Report
• PDB Structure of Molecule Inosine-5-Monophosphate Dehydrogenase
• Related Sequences
• Protein Family Classification
• Protein FamilySuperfamily Definitions
• Protein Domain Definition
• Superfamily-Domain-Motif Relationship
• iProClass Superfamily List
• iProClass Superfamily Report
• Alignment and Tree View
• PIR-Protein Sequence Database
• PIR-PSD Entry
• BLASTFASTA Search
• PIR FASTA Search Result
• PIR Searches and Aligment
• PIR Hidden Markov Model
• Bibliography Submission
• Bibliography Information Display (I)
• Bibliography Information Display (II)
• Oracle Demo
• Proteomic Bioinformatics

5

Peptide Search ResultsPeptide Search Results

6

PIR-NREF Search Result (I)PIR-NREF Search Result (I)Test Sequence ftpnbrfageorgetownedupirmisctestseq

7

PIR-NREF Search Result (II)PIR-NREF Search Result (II)

9

PIR Pattern SearchPIR Pattern Search

10

PIR Pattern Search Result (I)PIR Pattern Search Result (I)httppirgeorgetownedupirwwwsearchpatmatchhtml

Pattern Match Sequence vs PROSITE

11

PIR Pattern Search Result (II)PIR Pattern Search Result (II)bullSearch a query pattern against a sequence database

12

PIR Domain Display PIR Domain Display

13

PIR-NREF Database PIR-NREF Database (httppirgeorgetownedupirwwwsearchpirnrefshtml)(httppirgeorgetownedupirwwwsearchpirnrefshtml)

search

14

PIR-NREF ReportPIR-NREF Report

15

PIR-iProClass DatabasePIR-iProClass Database

16

iProClass Sequence ReportiProClass Sequence Report

17

PDB Structure of Molecule Inosine-PDB Structure of Molecule Inosine-5-Monophosphate Dehydrogenase5-Monophosphate Dehydrogenase

18

Related Sequences Related Sequences

19

Protein Family ClassificationProtein Family Classification

Superfamily Domain and Motif ClassificationSuperfamily Concept End-to-End Similarity amp Same Overall Domain Architecture

Significance Improve Sensitivity of Protein Identification Provide Complete Clustering for Database Organization Detect and Correct Genome Annotation Errors Systematically Drive Other Annotations Stimulate Evolution Genomics and Proteomics Research

Discovery of New Knowledge by Using Information Embedded within

Families of Homologous Sequences and Their Structures

20

Protein FamilySuperfamily DefinitionsProtein FamilySuperfamily Definitions

Family A Set of Protein Sequences That Share a Common

Evolutionary Ancestor with End-to-End Sequence Similarity (No Major Discrepancy by Standard Multiple Alignment Methods)

Have the Same Domain Architecture (Except Incomplete or Alternately Spliced)

Overall Sequence Identity gt=45

Superfamily A Set of Protein Families That Share a Common Evolutionary

Ancestor From End-to-end Have the Same Domain Architecture Overall Sequence Identity gt=20

21

Protein Domain DefinitionProtein Domain Definition

Homology Domain A Recognizable Region of Similarity Have a Common Ancestry Found in Diverse Protein Sequences (in gt= 2 Superfamilies)

A Sequence Can Belong to Only One Protein Family and Superfamily but May Contain More Than One Domains

22

Superfamily-Domain-Motif RelationshipSuperfamily-Domain-Motif Relationship

23

iProClass Superfamily ListiProClass Superfamily ListAll Superfamilies Containing PF00001

Superfamily-Domain Relationship ~6000 SFs have gt=1 DomainsSuperfamily for Domain Architecture

24

iProClass Superfamily ReportiProClass Superfamily Report

25

Alignment and Tree ViewAlignment and Tree View

26

PIR-Protein Sequence DatabasePIR-Protein Sequence Database

27

PIR-PSD EntryPIR-PSD Entry

28

BLASTFASTA SearchBLASTFASTA Search

29

PIR FASTA Search ResultPIR FASTA Search Result

30

PIR Searches and AligmentPIR Searches and Aligment BLAST Search

Multiple Alignment amp Tree View

31

PIR Hidden Markov ModelPIR Hidden Markov Modelhttppirgeorgetownedupirwwwsearchpirhmmhtml

HMM Model Building amp Sequence Search

One Protein Against All HMMs

All Proteins Against One HMM

33

Bibliography SubmissionBibliography Submission

View Bibliography Information

View Protein Entry

Submit Citation with Optional Categorization

S1

34

Bibliography Information Display (I)Bibliography Information Display (I)

From PIR-NREF

From Other Curated Database (eg SGD)

35

Bibliography Information Display (II)Bibliography Information Display (II)

From User Submission

From Computer-Mapping (eg Gene Symbol)

36

Oracle DemoOracle DemoJava Web Interface for Oracle Database Search (httppirgeorgetowneduiproclasshtml)

WebDB Interface to Oracle (WebDB) TablesViewsObjects FunctionsProceduresPackages

37

Proteomic BioinformaticsProteomic Bioinformatics

Large-Scale Analysis of Proteomic Data Homology Search for Pathways

• Database Demo
• PIR Web Site (httppirgeorgetownedu)
• Text Search Result with NULLNOT NULL
• Peptide Search Results
• PIR-NREF Search Result (I)
• PIR-NREF Search Result (II)
• PIR Pattern Search
• PIR Pattern Search Result (I)
• PIR Pattern Search Result (II)
• PIR Domain Display
• PIR-NREF Database (httppirgeorgetownedupirwwwsearchpirnrefshtml)
• PIR-NREF Report
• PIR-iProClass Database
• iProClass Sequence Report
• PDB Structure of Molecule Inosine-5-Monophosphate Dehydrogenase
• Related Sequences
• Protein Family Classification
• Protein FamilySuperfamily Definitions
• Protein Domain Definition
• Superfamily-Domain-Motif Relationship
• iProClass Superfamily List
• iProClass Superfamily Report
• Alignment and Tree View
• PIR-Protein Sequence Database
• PIR-PSD Entry
• BLASTFASTA Search
• PIR FASTA Search Result
• PIR Searches and Aligment
• PIR Hidden Markov Model
• Bibliography Submission
• Bibliography Information Display (I)
• Bibliography Information Display (II)
• Oracle Demo
• Proteomic Bioinformatics

6

PIR-NREF Search Result (I)PIR-NREF Search Result (I)Test Sequence ftpnbrfageorgetownedupirmisctestseq

7

PIR-NREF Search Result (II)PIR-NREF Search Result (II)

9

PIR Pattern SearchPIR Pattern Search

10

PIR Pattern Search Result (I)PIR Pattern Search Result (I)httppirgeorgetownedupirwwwsearchpatmatchhtml

Pattern Match Sequence vs PROSITE

11

PIR Pattern Search Result (II)PIR Pattern Search Result (II)bullSearch a query pattern against a sequence database

12

PIR Domain Display PIR Domain Display

13

PIR-NREF Database PIR-NREF Database (httppirgeorgetownedupirwwwsearchpirnrefshtml)(httppirgeorgetownedupirwwwsearchpirnrefshtml)

search

14

PIR-NREF ReportPIR-NREF Report

15

PIR-iProClass DatabasePIR-iProClass Database

16

iProClass Sequence ReportiProClass Sequence Report

17

PDB Structure of Molecule Inosine-PDB Structure of Molecule Inosine-5-Monophosphate Dehydrogenase5-Monophosphate Dehydrogenase

18

Related Sequences Related Sequences

19

Protein Family ClassificationProtein Family Classification

Superfamily Domain and Motif ClassificationSuperfamily Concept End-to-End Similarity amp Same Overall Domain Architecture

Significance Improve Sensitivity of Protein Identification Provide Complete Clustering for Database Organization Detect and Correct Genome Annotation Errors Systematically Drive Other Annotations Stimulate Evolution Genomics and Proteomics Research

Discovery of New Knowledge by Using Information Embedded within

Families of Homologous Sequences and Their Structures

20

Protein FamilySuperfamily DefinitionsProtein FamilySuperfamily Definitions

Family A Set of Protein Sequences That Share a Common

Evolutionary Ancestor with End-to-End Sequence Similarity (No Major Discrepancy by Standard Multiple Alignment Methods)

Have the Same Domain Architecture (Except Incomplete or Alternately Spliced)

Overall Sequence Identity gt=45

Superfamily A Set of Protein Families That Share a Common Evolutionary

Ancestor From End-to-end Have the Same Domain Architecture Overall Sequence Identity gt=20

21

Protein Domain DefinitionProtein Domain Definition

Homology Domain A Recognizable Region of Similarity Have a Common Ancestry Found in Diverse Protein Sequences (in gt= 2 Superfamilies)

A Sequence Can Belong to Only One Protein Family and Superfamily but May Contain More Than One Domains

22

Superfamily-Domain-Motif RelationshipSuperfamily-Domain-Motif Relationship

23

iProClass Superfamily ListiProClass Superfamily ListAll Superfamilies Containing PF00001

Superfamily-Domain Relationship ~6000 SFs have gt=1 DomainsSuperfamily for Domain Architecture

24

iProClass Superfamily ReportiProClass Superfamily Report

25

Alignment and Tree ViewAlignment and Tree View

26

PIR-Protein Sequence DatabasePIR-Protein Sequence Database

27

PIR-PSD EntryPIR-PSD Entry

28

BLASTFASTA SearchBLASTFASTA Search

29

PIR FASTA Search ResultPIR FASTA Search Result

30

PIR Searches and AligmentPIR Searches and Aligment BLAST Search

Multiple Alignment amp Tree View

31

PIR Hidden Markov ModelPIR Hidden Markov Modelhttppirgeorgetownedupirwwwsearchpirhmmhtml

HMM Model Building amp Sequence Search

One Protein Against All HMMs

All Proteins Against One HMM

33

Bibliography SubmissionBibliography Submission

View Bibliography Information

View Protein Entry

Submit Citation with Optional Categorization

S1

34

Bibliography Information Display (I)Bibliography Information Display (I)

From PIR-NREF

From Other Curated Database (eg SGD)

35

Bibliography Information Display (II)Bibliography Information Display (II)

From User Submission

From Computer-Mapping (eg Gene Symbol)

36

Oracle DemoOracle DemoJava Web Interface for Oracle Database Search (httppirgeorgetowneduiproclasshtml)

WebDB Interface to Oracle (WebDB) TablesViewsObjects FunctionsProceduresPackages

37

Proteomic BioinformaticsProteomic Bioinformatics

Large-Scale Analysis of Proteomic Data Homology Search for Pathways

• Database Demo
• PIR Web Site (httppirgeorgetownedu)
• Text Search Result with NULLNOT NULL
• Peptide Search Results
• PIR-NREF Search Result (I)
• PIR-NREF Search Result (II)
• PIR Pattern Search
• PIR Pattern Search Result (I)
• PIR Pattern Search Result (II)
• PIR Domain Display
• PIR-NREF Database (httppirgeorgetownedupirwwwsearchpirnrefshtml)
• PIR-NREF Report
• PIR-iProClass Database
• iProClass Sequence Report
• PDB Structure of Molecule Inosine-5-Monophosphate Dehydrogenase
• Related Sequences
• Protein Family Classification
• Protein FamilySuperfamily Definitions
• Protein Domain Definition
• Superfamily-Domain-Motif Relationship
• iProClass Superfamily List
• iProClass Superfamily Report
• Alignment and Tree View
• PIR-Protein Sequence Database
• PIR-PSD Entry
• BLASTFASTA Search
• PIR FASTA Search Result
• PIR Searches and Aligment
• PIR Hidden Markov Model
• Bibliography Submission
• Bibliography Information Display (I)
• Bibliography Information Display (II)
• Oracle Demo
• Proteomic Bioinformatics

7

PIR-NREF Search Result (II)PIR-NREF Search Result (II)

9

PIR Pattern SearchPIR Pattern Search

10

PIR Pattern Search Result (I)PIR Pattern Search Result (I)httppirgeorgetownedupirwwwsearchpatmatchhtml

Pattern Match Sequence vs PROSITE

11

PIR Pattern Search Result (II)PIR Pattern Search Result (II)bullSearch a query pattern against a sequence database

12

PIR Domain Display PIR Domain Display

13

PIR-NREF Database PIR-NREF Database (httppirgeorgetownedupirwwwsearchpirnrefshtml)(httppirgeorgetownedupirwwwsearchpirnrefshtml)

search

14

PIR-NREF ReportPIR-NREF Report

15

PIR-iProClass DatabasePIR-iProClass Database

16

iProClass Sequence ReportiProClass Sequence Report

17

PDB Structure of Molecule Inosine-PDB Structure of Molecule Inosine-5-Monophosphate Dehydrogenase5-Monophosphate Dehydrogenase

18

Related Sequences Related Sequences

19

Protein Family ClassificationProtein Family Classification

Superfamily Domain and Motif ClassificationSuperfamily Concept End-to-End Similarity amp Same Overall Domain Architecture

Significance Improve Sensitivity of Protein Identification Provide Complete Clustering for Database Organization Detect and Correct Genome Annotation Errors Systematically Drive Other Annotations Stimulate Evolution Genomics and Proteomics Research

Discovery of New Knowledge by Using Information Embedded within

Families of Homologous Sequences and Their Structures

20

Protein FamilySuperfamily DefinitionsProtein FamilySuperfamily Definitions

Family A Set of Protein Sequences That Share a Common

Evolutionary Ancestor with End-to-End Sequence Similarity (No Major Discrepancy by Standard Multiple Alignment Methods)

Have the Same Domain Architecture (Except Incomplete or Alternately Spliced)

Overall Sequence Identity gt=45

Superfamily A Set of Protein Families That Share a Common Evolutionary

Ancestor From End-to-end Have the Same Domain Architecture Overall Sequence Identity gt=20

21

Protein Domain DefinitionProtein Domain Definition

Homology Domain A Recognizable Region of Similarity Have a Common Ancestry Found in Diverse Protein Sequences (in gt= 2 Superfamilies)

A Sequence Can Belong to Only One Protein Family and Superfamily but May Contain More Than One Domains

22

Superfamily-Domain-Motif RelationshipSuperfamily-Domain-Motif Relationship

23

iProClass Superfamily ListiProClass Superfamily ListAll Superfamilies Containing PF00001

Superfamily-Domain Relationship ~6000 SFs have gt=1 DomainsSuperfamily for Domain Architecture

24

iProClass Superfamily ReportiProClass Superfamily Report

25

Alignment and Tree ViewAlignment and Tree View

26

PIR-Protein Sequence DatabasePIR-Protein Sequence Database

27

PIR-PSD EntryPIR-PSD Entry

28

BLASTFASTA SearchBLASTFASTA Search

29

PIR FASTA Search ResultPIR FASTA Search Result

30

PIR Searches and AligmentPIR Searches and Aligment BLAST Search

Multiple Alignment amp Tree View

31

PIR Hidden Markov ModelPIR Hidden Markov Modelhttppirgeorgetownedupirwwwsearchpirhmmhtml

HMM Model Building amp Sequence Search

One Protein Against All HMMs

All Proteins Against One HMM

33

Bibliography SubmissionBibliography Submission

View Bibliography Information

View Protein Entry

Submit Citation with Optional Categorization

S1

34

Bibliography Information Display (I)Bibliography Information Display (I)

From PIR-NREF

From Other Curated Database (eg SGD)

35

Bibliography Information Display (II)Bibliography Information Display (II)

From User Submission

From Computer-Mapping (eg Gene Symbol)

36

Oracle DemoOracle DemoJava Web Interface for Oracle Database Search (httppirgeorgetowneduiproclasshtml)

WebDB Interface to Oracle (WebDB) TablesViewsObjects FunctionsProceduresPackages

37

Proteomic BioinformaticsProteomic Bioinformatics

Large-Scale Analysis of Proteomic Data Homology Search for Pathways

• Database Demo
• PIR Web Site (httppirgeorgetownedu)
• Text Search Result with NULLNOT NULL
• Peptide Search Results
• PIR-NREF Search Result (I)
• PIR-NREF Search Result (II)
• PIR Pattern Search
• PIR Pattern Search Result (I)
• PIR Pattern Search Result (II)
• PIR Domain Display
• PIR-NREF Database (httppirgeorgetownedupirwwwsearchpirnrefshtml)
• PIR-NREF Report
• PIR-iProClass Database
• iProClass Sequence Report
• PDB Structure of Molecule Inosine-5-Monophosphate Dehydrogenase
• Related Sequences
• Protein Family Classification
• Protein FamilySuperfamily Definitions
• Protein Domain Definition
• Superfamily-Domain-Motif Relationship
• iProClass Superfamily List
• iProClass Superfamily Report
• Alignment and Tree View
• PIR-Protein Sequence Database
• PIR-PSD Entry
• BLASTFASTA Search
• PIR FASTA Search Result
• PIR Searches and Aligment
• PIR Hidden Markov Model
• Bibliography Submission
• Bibliography Information Display (I)
• Bibliography Information Display (II)
• Oracle Demo
• Proteomic Bioinformatics

9

PIR Pattern SearchPIR Pattern Search

10

PIR Pattern Search Result (I)PIR Pattern Search Result (I)httppirgeorgetownedupirwwwsearchpatmatchhtml

Pattern Match Sequence vs PROSITE

11

PIR Pattern Search Result (II)PIR Pattern Search Result (II)bullSearch a query pattern against a sequence database

12

PIR Domain Display PIR Domain Display

13

PIR-NREF Database PIR-NREF Database (httppirgeorgetownedupirwwwsearchpirnrefshtml)(httppirgeorgetownedupirwwwsearchpirnrefshtml)

search

14

PIR-NREF ReportPIR-NREF Report

15

PIR-iProClass DatabasePIR-iProClass Database

16

iProClass Sequence ReportiProClass Sequence Report

17

PDB Structure of Molecule Inosine-PDB Structure of Molecule Inosine-5-Monophosphate Dehydrogenase5-Monophosphate Dehydrogenase

18

Related Sequences Related Sequences

19

Protein Family ClassificationProtein Family Classification

Superfamily Domain and Motif ClassificationSuperfamily Concept End-to-End Similarity amp Same Overall Domain Architecture

Significance Improve Sensitivity of Protein Identification Provide Complete Clustering for Database Organization Detect and Correct Genome Annotation Errors Systematically Drive Other Annotations Stimulate Evolution Genomics and Proteomics Research

Discovery of New Knowledge by Using Information Embedded within

Families of Homologous Sequences and Their Structures

20

Protein FamilySuperfamily DefinitionsProtein FamilySuperfamily Definitions

Family A Set of Protein Sequences That Share a Common

Evolutionary Ancestor with End-to-End Sequence Similarity (No Major Discrepancy by Standard Multiple Alignment Methods)

Have the Same Domain Architecture (Except Incomplete or Alternately Spliced)

Overall Sequence Identity gt=45

Superfamily A Set of Protein Families That Share a Common Evolutionary

Ancestor From End-to-end Have the Same Domain Architecture Overall Sequence Identity gt=20

21

Protein Domain DefinitionProtein Domain Definition

Homology Domain A Recognizable Region of Similarity Have a Common Ancestry Found in Diverse Protein Sequences (in gt= 2 Superfamilies)

A Sequence Can Belong to Only One Protein Family and Superfamily but May Contain More Than One Domains

22

Superfamily-Domain-Motif RelationshipSuperfamily-Domain-Motif Relationship

23

iProClass Superfamily ListiProClass Superfamily ListAll Superfamilies Containing PF00001

Superfamily-Domain Relationship ~6000 SFs have gt=1 DomainsSuperfamily for Domain Architecture

24

iProClass Superfamily ReportiProClass Superfamily Report

25

Alignment and Tree ViewAlignment and Tree View

26

PIR-Protein Sequence DatabasePIR-Protein Sequence Database

27

PIR-PSD EntryPIR-PSD Entry

28

BLASTFASTA SearchBLASTFASTA Search

29

PIR FASTA Search ResultPIR FASTA Search Result

30

PIR Searches and AligmentPIR Searches and Aligment BLAST Search

Multiple Alignment amp Tree View

31

PIR Hidden Markov ModelPIR Hidden Markov Modelhttppirgeorgetownedupirwwwsearchpirhmmhtml

HMM Model Building amp Sequence Search

One Protein Against All HMMs

All Proteins Against One HMM

33

Bibliography SubmissionBibliography Submission

View Bibliography Information

View Protein Entry

Submit Citation with Optional Categorization

S1

34

Bibliography Information Display (I)Bibliography Information Display (I)

From PIR-NREF

From Other Curated Database (eg SGD)

35

Bibliography Information Display (II)Bibliography Information Display (II)

From User Submission

From Computer-Mapping (eg Gene Symbol)

36

Oracle DemoOracle DemoJava Web Interface for Oracle Database Search (httppirgeorgetowneduiproclasshtml)

WebDB Interface to Oracle (WebDB) TablesViewsObjects FunctionsProceduresPackages

37

Proteomic BioinformaticsProteomic Bioinformatics

Large-Scale Analysis of Proteomic Data Homology Search for Pathways

• Database Demo
• PIR Web Site (httppirgeorgetownedu)
• Text Search Result with NULLNOT NULL
• Peptide Search Results
• PIR-NREF Search Result (I)
• PIR-NREF Search Result (II)
• PIR Pattern Search
• PIR Pattern Search Result (I)
• PIR Pattern Search Result (II)
• PIR Domain Display
• PIR-NREF Database (httppirgeorgetownedupirwwwsearchpirnrefshtml)
• PIR-NREF Report
• PIR-iProClass Database
• iProClass Sequence Report
• PDB Structure of Molecule Inosine-5-Monophosphate Dehydrogenase
• Related Sequences
• Protein Family Classification
• Protein FamilySuperfamily Definitions
• Protein Domain Definition
• Superfamily-Domain-Motif Relationship
• iProClass Superfamily List
• iProClass Superfamily Report
• Alignment and Tree View
• PIR-Protein Sequence Database
• PIR-PSD Entry
• BLASTFASTA Search
• PIR FASTA Search Result
• PIR Searches and Aligment
• PIR Hidden Markov Model
• Bibliography Submission
• Bibliography Information Display (I)
• Bibliography Information Display (II)
• Oracle Demo
• Proteomic Bioinformatics

10

PIR Pattern Search Result (I)PIR Pattern Search Result (I)httppirgeorgetownedupirwwwsearchpatmatchhtml

Pattern Match Sequence vs PROSITE

11

PIR Pattern Search Result (II)PIR Pattern Search Result (II)bullSearch a query pattern against a sequence database

12

PIR Domain Display PIR Domain Display

13

PIR-NREF Database PIR-NREF Database (httppirgeorgetownedupirwwwsearchpirnrefshtml)(httppirgeorgetownedupirwwwsearchpirnrefshtml)

search

14

PIR-NREF ReportPIR-NREF Report

15

PIR-iProClass DatabasePIR-iProClass Database

16

iProClass Sequence ReportiProClass Sequence Report

17

PDB Structure of Molecule Inosine-PDB Structure of Molecule Inosine-5-Monophosphate Dehydrogenase5-Monophosphate Dehydrogenase

18

Related Sequences Related Sequences

19

Protein Family ClassificationProtein Family Classification

Superfamily Domain and Motif ClassificationSuperfamily Concept End-to-End Similarity amp Same Overall Domain Architecture

Significance Improve Sensitivity of Protein Identification Provide Complete Clustering for Database Organization Detect and Correct Genome Annotation Errors Systematically Drive Other Annotations Stimulate Evolution Genomics and Proteomics Research

Discovery of New Knowledge by Using Information Embedded within

Families of Homologous Sequences and Their Structures

20

Protein FamilySuperfamily DefinitionsProtein FamilySuperfamily Definitions

Family A Set of Protein Sequences That Share a Common

Evolutionary Ancestor with End-to-End Sequence Similarity (No Major Discrepancy by Standard Multiple Alignment Methods)

Have the Same Domain Architecture (Except Incomplete or Alternately Spliced)

Overall Sequence Identity gt=45

Superfamily A Set of Protein Families That Share a Common Evolutionary

Ancestor From End-to-end Have the Same Domain Architecture Overall Sequence Identity gt=20

21

Protein Domain DefinitionProtein Domain Definition

Homology Domain A Recognizable Region of Similarity Have a Common Ancestry Found in Diverse Protein Sequences (in gt= 2 Superfamilies)

A Sequence Can Belong to Only One Protein Family and Superfamily but May Contain More Than One Domains

22

Superfamily-Domain-Motif RelationshipSuperfamily-Domain-Motif Relationship

23

iProClass Superfamily ListiProClass Superfamily ListAll Superfamilies Containing PF00001

Superfamily-Domain Relationship ~6000 SFs have gt=1 DomainsSuperfamily for Domain Architecture

24

iProClass Superfamily ReportiProClass Superfamily Report

25

Alignment and Tree ViewAlignment and Tree View

26

PIR-Protein Sequence DatabasePIR-Protein Sequence Database

27

PIR-PSD EntryPIR-PSD Entry

28

BLASTFASTA SearchBLASTFASTA Search

29

PIR FASTA Search ResultPIR FASTA Search Result

30

PIR Searches and AligmentPIR Searches and Aligment BLAST Search

Multiple Alignment amp Tree View

31

PIR Hidden Markov ModelPIR Hidden Markov Modelhttppirgeorgetownedupirwwwsearchpirhmmhtml

HMM Model Building amp Sequence Search

One Protein Against All HMMs

All Proteins Against One HMM

33

Bibliography SubmissionBibliography Submission

View Bibliography Information

View Protein Entry

Submit Citation with Optional Categorization

S1

34

Bibliography Information Display (I)Bibliography Information Display (I)

From PIR-NREF

From Other Curated Database (eg SGD)

35

Bibliography Information Display (II)Bibliography Information Display (II)

From User Submission

From Computer-Mapping (eg Gene Symbol)

36

Oracle DemoOracle DemoJava Web Interface for Oracle Database Search (httppirgeorgetowneduiproclasshtml)

WebDB Interface to Oracle (WebDB) TablesViewsObjects FunctionsProceduresPackages

37

Proteomic BioinformaticsProteomic Bioinformatics

Large-Scale Analysis of Proteomic Data Homology Search for Pathways

• Database Demo
• PIR Web Site (httppirgeorgetownedu)
• Text Search Result with NULLNOT NULL
• Peptide Search Results
• PIR-NREF Search Result (I)
• PIR-NREF Search Result (II)
• PIR Pattern Search
• PIR Pattern Search Result (I)
• PIR Pattern Search Result (II)
• PIR Domain Display
• PIR-NREF Database (httppirgeorgetownedupirwwwsearchpirnrefshtml)
• PIR-NREF Report
• PIR-iProClass Database
• iProClass Sequence Report
• PDB Structure of Molecule Inosine-5-Monophosphate Dehydrogenase
• Related Sequences
• Protein Family Classification
• Protein FamilySuperfamily Definitions
• Protein Domain Definition
• Superfamily-Domain-Motif Relationship
• iProClass Superfamily List
• iProClass Superfamily Report
• Alignment and Tree View
• PIR-Protein Sequence Database
• PIR-PSD Entry
• BLASTFASTA Search
• PIR FASTA Search Result
• PIR Searches and Aligment
• PIR Hidden Markov Model
• Bibliography Submission
• Bibliography Information Display (I)
• Bibliography Information Display (II)
• Oracle Demo
• Proteomic Bioinformatics

11

PIR Pattern Search Result (II)PIR Pattern Search Result (II)bullSearch a query pattern against a sequence database

12

PIR Domain Display PIR Domain Display

13

PIR-NREF Database PIR-NREF Database (httppirgeorgetownedupirwwwsearchpirnrefshtml)(httppirgeorgetownedupirwwwsearchpirnrefshtml)

search

14

PIR-NREF ReportPIR-NREF Report

15

PIR-iProClass DatabasePIR-iProClass Database

16

iProClass Sequence ReportiProClass Sequence Report

17

PDB Structure of Molecule Inosine-PDB Structure of Molecule Inosine-5-Monophosphate Dehydrogenase5-Monophosphate Dehydrogenase

18

Related Sequences Related Sequences

19

Protein Family ClassificationProtein Family Classification

Superfamily Domain and Motif ClassificationSuperfamily Concept End-to-End Similarity amp Same Overall Domain Architecture

Significance Improve Sensitivity of Protein Identification Provide Complete Clustering for Database Organization Detect and Correct Genome Annotation Errors Systematically Drive Other Annotations Stimulate Evolution Genomics and Proteomics Research

Discovery of New Knowledge by Using Information Embedded within

Families of Homologous Sequences and Their Structures

20

Protein FamilySuperfamily DefinitionsProtein FamilySuperfamily Definitions

Family A Set of Protein Sequences That Share a Common

Evolutionary Ancestor with End-to-End Sequence Similarity (No Major Discrepancy by Standard Multiple Alignment Methods)

Have the Same Domain Architecture (Except Incomplete or Alternately Spliced)

Overall Sequence Identity gt=45

Superfamily A Set of Protein Families That Share a Common Evolutionary

Ancestor From End-to-end Have the Same Domain Architecture Overall Sequence Identity gt=20

21

Protein Domain DefinitionProtein Domain Definition

Homology Domain A Recognizable Region of Similarity Have a Common Ancestry Found in Diverse Protein Sequences (in gt= 2 Superfamilies)

A Sequence Can Belong to Only One Protein Family and Superfamily but May Contain More Than One Domains

22

Superfamily-Domain-Motif RelationshipSuperfamily-Domain-Motif Relationship

23

iProClass Superfamily ListiProClass Superfamily ListAll Superfamilies Containing PF00001

Superfamily-Domain Relationship ~6000 SFs have gt=1 DomainsSuperfamily for Domain Architecture

24

iProClass Superfamily ReportiProClass Superfamily Report

25

Alignment and Tree ViewAlignment and Tree View

26

PIR-Protein Sequence DatabasePIR-Protein Sequence Database

27

PIR-PSD EntryPIR-PSD Entry

28

BLASTFASTA SearchBLASTFASTA Search

29

PIR FASTA Search ResultPIR FASTA Search Result

30

PIR Searches and AligmentPIR Searches and Aligment BLAST Search

Multiple Alignment amp Tree View

31

PIR Hidden Markov ModelPIR Hidden Markov Modelhttppirgeorgetownedupirwwwsearchpirhmmhtml

HMM Model Building amp Sequence Search

One Protein Against All HMMs

All Proteins Against One HMM

33

Bibliography SubmissionBibliography Submission

View Bibliography Information

View Protein Entry

Submit Citation with Optional Categorization

S1

34

Bibliography Information Display (I)Bibliography Information Display (I)

From PIR-NREF

From Other Curated Database (eg SGD)

35

Bibliography Information Display (II)Bibliography Information Display (II)

From User Submission

From Computer-Mapping (eg Gene Symbol)

36

Oracle DemoOracle DemoJava Web Interface for Oracle Database Search (httppirgeorgetowneduiproclasshtml)

WebDB Interface to Oracle (WebDB) TablesViewsObjects FunctionsProceduresPackages

37

Proteomic BioinformaticsProteomic Bioinformatics

Large-Scale Analysis of Proteomic Data Homology Search for Pathways

• Database Demo
• PIR Web Site (httppirgeorgetownedu)
• Text Search Result with NULLNOT NULL
• Peptide Search Results
• PIR-NREF Search Result (I)
• PIR-NREF Search Result (II)
• PIR Pattern Search
• PIR Pattern Search Result (I)
• PIR Pattern Search Result (II)
• PIR Domain Display
• PIR-NREF Database (httppirgeorgetownedupirwwwsearchpirnrefshtml)
• PIR-NREF Report
• PIR-iProClass Database
• iProClass Sequence Report
• PDB Structure of Molecule Inosine-5-Monophosphate Dehydrogenase
• Related Sequences
• Protein Family Classification
• Protein FamilySuperfamily Definitions
• Protein Domain Definition
• Superfamily-Domain-Motif Relationship
• iProClass Superfamily List
• iProClass Superfamily Report
• Alignment and Tree View
• PIR-Protein Sequence Database
• PIR-PSD Entry
• BLASTFASTA Search
• PIR FASTA Search Result
• PIR Searches and Aligment
• PIR Hidden Markov Model
• Bibliography Submission
• Bibliography Information Display (I)
• Bibliography Information Display (II)
• Oracle Demo
• Proteomic Bioinformatics

12

PIR Domain Display PIR Domain Display

13

PIR-NREF Database PIR-NREF Database (httppirgeorgetownedupirwwwsearchpirnrefshtml)(httppirgeorgetownedupirwwwsearchpirnrefshtml)

search

14

PIR-NREF ReportPIR-NREF Report

15

PIR-iProClass DatabasePIR-iProClass Database

16

iProClass Sequence ReportiProClass Sequence Report

17

PDB Structure of Molecule Inosine-PDB Structure of Molecule Inosine-5-Monophosphate Dehydrogenase5-Monophosphate Dehydrogenase

18

Related Sequences Related Sequences

19

Protein Family ClassificationProtein Family Classification

Superfamily Domain and Motif ClassificationSuperfamily Concept End-to-End Similarity amp Same Overall Domain Architecture

Significance Improve Sensitivity of Protein Identification Provide Complete Clustering for Database Organization Detect and Correct Genome Annotation Errors Systematically Drive Other Annotations Stimulate Evolution Genomics and Proteomics Research

Discovery of New Knowledge by Using Information Embedded within

Families of Homologous Sequences and Their Structures

20

Protein FamilySuperfamily DefinitionsProtein FamilySuperfamily Definitions

Family A Set of Protein Sequences That Share a Common

Evolutionary Ancestor with End-to-End Sequence Similarity (No Major Discrepancy by Standard Multiple Alignment Methods)

Have the Same Domain Architecture (Except Incomplete or Alternately Spliced)

Overall Sequence Identity gt=45

Superfamily A Set of Protein Families That Share a Common Evolutionary

Ancestor From End-to-end Have the Same Domain Architecture Overall Sequence Identity gt=20

21

Protein Domain DefinitionProtein Domain Definition

Homology Domain A Recognizable Region of Similarity Have a Common Ancestry Found in Diverse Protein Sequences (in gt= 2 Superfamilies)

A Sequence Can Belong to Only One Protein Family and Superfamily but May Contain More Than One Domains

22

Superfamily-Domain-Motif RelationshipSuperfamily-Domain-Motif Relationship

23

iProClass Superfamily ListiProClass Superfamily ListAll Superfamilies Containing PF00001

Superfamily-Domain Relationship ~6000 SFs have gt=1 DomainsSuperfamily for Domain Architecture

24

iProClass Superfamily ReportiProClass Superfamily Report

25

Alignment and Tree ViewAlignment and Tree View

26

PIR-Protein Sequence DatabasePIR-Protein Sequence Database

27

PIR-PSD EntryPIR-PSD Entry

28

BLASTFASTA SearchBLASTFASTA Search

29

PIR FASTA Search ResultPIR FASTA Search Result

30

PIR Searches and AligmentPIR Searches and Aligment BLAST Search

Multiple Alignment amp Tree View

31

PIR Hidden Markov ModelPIR Hidden Markov Modelhttppirgeorgetownedupirwwwsearchpirhmmhtml

HMM Model Building amp Sequence Search

One Protein Against All HMMs

All Proteins Against One HMM

33

Bibliography SubmissionBibliography Submission

View Bibliography Information

View Protein Entry

Submit Citation with Optional Categorization

S1

34

Bibliography Information Display (I)Bibliography Information Display (I)

From PIR-NREF

From Other Curated Database (eg SGD)

35

Bibliography Information Display (II)Bibliography Information Display (II)

From User Submission

From Computer-Mapping (eg Gene Symbol)

36

Oracle DemoOracle DemoJava Web Interface for Oracle Database Search (httppirgeorgetowneduiproclasshtml)

WebDB Interface to Oracle (WebDB) TablesViewsObjects FunctionsProceduresPackages

37

Proteomic BioinformaticsProteomic Bioinformatics

Large-Scale Analysis of Proteomic Data Homology Search for Pathways

• Database Demo
• PIR Web Site (httppirgeorgetownedu)
• Text Search Result with NULLNOT NULL
• Peptide Search Results
• PIR-NREF Search Result (I)
• PIR-NREF Search Result (II)
• PIR Pattern Search
• PIR Pattern Search Result (I)
• PIR Pattern Search Result (II)
• PIR Domain Display
• PIR-NREF Database (httppirgeorgetownedupirwwwsearchpirnrefshtml)
• PIR-NREF Report
• PIR-iProClass Database
• iProClass Sequence Report
• PDB Structure of Molecule Inosine-5-Monophosphate Dehydrogenase
• Related Sequences
• Protein Family Classification
• Protein FamilySuperfamily Definitions
• Protein Domain Definition
• Superfamily-Domain-Motif Relationship
• iProClass Superfamily List
• iProClass Superfamily Report
• Alignment and Tree View
• PIR-Protein Sequence Database
• PIR-PSD Entry
• BLASTFASTA Search
• PIR FASTA Search Result
• PIR Searches and Aligment
• PIR Hidden Markov Model
• Bibliography Submission
• Bibliography Information Display (I)
• Bibliography Information Display (II)
• Oracle Demo
• Proteomic Bioinformatics

13

PIR-NREF Database PIR-NREF Database (httppirgeorgetownedupirwwwsearchpirnrefshtml)(httppirgeorgetownedupirwwwsearchpirnrefshtml)

search

14

PIR-NREF ReportPIR-NREF Report

15

PIR-iProClass DatabasePIR-iProClass Database

16

iProClass Sequence ReportiProClass Sequence Report

17

PDB Structure of Molecule Inosine-PDB Structure of Molecule Inosine-5-Monophosphate Dehydrogenase5-Monophosphate Dehydrogenase

18

Related Sequences Related Sequences

19

Protein Family ClassificationProtein Family Classification

Superfamily Domain and Motif ClassificationSuperfamily Concept End-to-End Similarity amp Same Overall Domain Architecture

Significance Improve Sensitivity of Protein Identification Provide Complete Clustering for Database Organization Detect and Correct Genome Annotation Errors Systematically Drive Other Annotations Stimulate Evolution Genomics and Proteomics Research

Discovery of New Knowledge by Using Information Embedded within

Families of Homologous Sequences and Their Structures

20

Protein FamilySuperfamily DefinitionsProtein FamilySuperfamily Definitions

Family A Set of Protein Sequences That Share a Common

Evolutionary Ancestor with End-to-End Sequence Similarity (No Major Discrepancy by Standard Multiple Alignment Methods)

Have the Same Domain Architecture (Except Incomplete or Alternately Spliced)

Overall Sequence Identity gt=45

Superfamily A Set of Protein Families That Share a Common Evolutionary

Ancestor From End-to-end Have the Same Domain Architecture Overall Sequence Identity gt=20

21

Protein Domain DefinitionProtein Domain Definition

Homology Domain A Recognizable Region of Similarity Have a Common Ancestry Found in Diverse Protein Sequences (in gt= 2 Superfamilies)

A Sequence Can Belong to Only One Protein Family and Superfamily but May Contain More Than One Domains

22

Superfamily-Domain-Motif RelationshipSuperfamily-Domain-Motif Relationship

23

iProClass Superfamily ListiProClass Superfamily ListAll Superfamilies Containing PF00001

Superfamily-Domain Relationship ~6000 SFs have gt=1 DomainsSuperfamily for Domain Architecture

24

iProClass Superfamily ReportiProClass Superfamily Report

25

Alignment and Tree ViewAlignment and Tree View

26

PIR-Protein Sequence DatabasePIR-Protein Sequence Database

27

PIR-PSD EntryPIR-PSD Entry

28

BLASTFASTA SearchBLASTFASTA Search

29

PIR FASTA Search ResultPIR FASTA Search Result

30

PIR Searches and AligmentPIR Searches and Aligment BLAST Search

Multiple Alignment amp Tree View

31

PIR Hidden Markov ModelPIR Hidden Markov Modelhttppirgeorgetownedupirwwwsearchpirhmmhtml

HMM Model Building amp Sequence Search

One Protein Against All HMMs

All Proteins Against One HMM

33

Bibliography SubmissionBibliography Submission

View Bibliography Information

View Protein Entry

Submit Citation with Optional Categorization

S1

34

Bibliography Information Display (I)Bibliography Information Display (I)

From PIR-NREF

From Other Curated Database (eg SGD)

35

Bibliography Information Display (II)Bibliography Information Display (II)

From User Submission

From Computer-Mapping (eg Gene Symbol)

36

Oracle DemoOracle DemoJava Web Interface for Oracle Database Search (httppirgeorgetowneduiproclasshtml)

WebDB Interface to Oracle (WebDB) TablesViewsObjects FunctionsProceduresPackages

37

Proteomic BioinformaticsProteomic Bioinformatics

Large-Scale Analysis of Proteomic Data Homology Search for Pathways

• Database Demo
• PIR Web Site (httppirgeorgetownedu)
• Text Search Result with NULLNOT NULL
• Peptide Search Results
• PIR-NREF Search Result (I)
• PIR-NREF Search Result (II)
• PIR Pattern Search
• PIR Pattern Search Result (I)
• PIR Pattern Search Result (II)
• PIR Domain Display
• PIR-NREF Database (httppirgeorgetownedupirwwwsearchpirnrefshtml)
• PIR-NREF Report
• PIR-iProClass Database
• iProClass Sequence Report
• PDB Structure of Molecule Inosine-5-Monophosphate Dehydrogenase
• Related Sequences
• Protein Family Classification
• Protein FamilySuperfamily Definitions
• Protein Domain Definition
• Superfamily-Domain-Motif Relationship
• iProClass Superfamily List
• iProClass Superfamily Report
• Alignment and Tree View
• PIR-Protein Sequence Database
• PIR-PSD Entry
• BLASTFASTA Search
• PIR FASTA Search Result
• PIR Searches and Aligment
• PIR Hidden Markov Model
• Bibliography Submission
• Bibliography Information Display (I)
• Bibliography Information Display (II)
• Oracle Demo
• Proteomic Bioinformatics

14

PIR-NREF ReportPIR-NREF Report

15

PIR-iProClass DatabasePIR-iProClass Database

16

iProClass Sequence ReportiProClass Sequence Report

17

PDB Structure of Molecule Inosine-PDB Structure of Molecule Inosine-5-Monophosphate Dehydrogenase5-Monophosphate Dehydrogenase

18

Related Sequences Related Sequences

19

Protein Family ClassificationProtein Family Classification

Superfamily Domain and Motif ClassificationSuperfamily Concept End-to-End Similarity amp Same Overall Domain Architecture

Significance Improve Sensitivity of Protein Identification Provide Complete Clustering for Database Organization Detect and Correct Genome Annotation Errors Systematically Drive Other Annotations Stimulate Evolution Genomics and Proteomics Research

Discovery of New Knowledge by Using Information Embedded within

Families of Homologous Sequences and Their Structures

20

Protein FamilySuperfamily DefinitionsProtein FamilySuperfamily Definitions

Family A Set of Protein Sequences That Share a Common

Evolutionary Ancestor with End-to-End Sequence Similarity (No Major Discrepancy by Standard Multiple Alignment Methods)

Have the Same Domain Architecture (Except Incomplete or Alternately Spliced)

Overall Sequence Identity gt=45

Superfamily A Set of Protein Families That Share a Common Evolutionary

Ancestor From End-to-end Have the Same Domain Architecture Overall Sequence Identity gt=20

21

Protein Domain DefinitionProtein Domain Definition

Homology Domain A Recognizable Region of Similarity Have a Common Ancestry Found in Diverse Protein Sequences (in gt= 2 Superfamilies)

A Sequence Can Belong to Only One Protein Family and Superfamily but May Contain More Than One Domains

22

Superfamily-Domain-Motif RelationshipSuperfamily-Domain-Motif Relationship

23

iProClass Superfamily ListiProClass Superfamily ListAll Superfamilies Containing PF00001

Superfamily-Domain Relationship ~6000 SFs have gt=1 DomainsSuperfamily for Domain Architecture

24

iProClass Superfamily ReportiProClass Superfamily Report

25

Alignment and Tree ViewAlignment and Tree View

26

PIR-Protein Sequence DatabasePIR-Protein Sequence Database

27

PIR-PSD EntryPIR-PSD Entry

28

BLASTFASTA SearchBLASTFASTA Search

29

PIR FASTA Search ResultPIR FASTA Search Result

30

PIR Searches and AligmentPIR Searches and Aligment BLAST Search

Multiple Alignment amp Tree View

31

PIR Hidden Markov ModelPIR Hidden Markov Modelhttppirgeorgetownedupirwwwsearchpirhmmhtml

HMM Model Building amp Sequence Search

One Protein Against All HMMs

All Proteins Against One HMM

33

Bibliography SubmissionBibliography Submission

View Bibliography Information

View Protein Entry

Submit Citation with Optional Categorization

S1

34

Bibliography Information Display (I)Bibliography Information Display (I)

From PIR-NREF

From Other Curated Database (eg SGD)

35

Bibliography Information Display (II)Bibliography Information Display (II)

From User Submission

From Computer-Mapping (eg Gene Symbol)

36

Oracle DemoOracle DemoJava Web Interface for Oracle Database Search (httppirgeorgetowneduiproclasshtml)

WebDB Interface to Oracle (WebDB) TablesViewsObjects FunctionsProceduresPackages

37

Proteomic BioinformaticsProteomic Bioinformatics

Large-Scale Analysis of Proteomic Data Homology Search for Pathways

• Database Demo
• PIR Web Site (httppirgeorgetownedu)
• Text Search Result with NULLNOT NULL
• Peptide Search Results
• PIR-NREF Search Result (I)
• PIR-NREF Search Result (II)
• PIR Pattern Search
• PIR Pattern Search Result (I)
• PIR Pattern Search Result (II)
• PIR Domain Display
• PIR-NREF Database (httppirgeorgetownedupirwwwsearchpirnrefshtml)
• PIR-NREF Report
• PIR-iProClass Database
• iProClass Sequence Report
• PDB Structure of Molecule Inosine-5-Monophosphate Dehydrogenase
• Related Sequences
• Protein Family Classification
• Protein FamilySuperfamily Definitions
• Protein Domain Definition
• Superfamily-Domain-Motif Relationship
• iProClass Superfamily List
• iProClass Superfamily Report
• Alignment and Tree View
• PIR-Protein Sequence Database
• PIR-PSD Entry
• BLASTFASTA Search
• PIR FASTA Search Result
• PIR Searches and Aligment
• PIR Hidden Markov Model
• Bibliography Submission
• Bibliography Information Display (I)
• Bibliography Information Display (II)
• Oracle Demo
• Proteomic Bioinformatics

15

PIR-iProClass DatabasePIR-iProClass Database

16

iProClass Sequence ReportiProClass Sequence Report

17

PDB Structure of Molecule Inosine-PDB Structure of Molecule Inosine-5-Monophosphate Dehydrogenase5-Monophosphate Dehydrogenase

18

Related Sequences Related Sequences

19

Protein Family ClassificationProtein Family Classification

Superfamily Domain and Motif ClassificationSuperfamily Concept End-to-End Similarity amp Same Overall Domain Architecture

Significance Improve Sensitivity of Protein Identification Provide Complete Clustering for Database Organization Detect and Correct Genome Annotation Errors Systematically Drive Other Annotations Stimulate Evolution Genomics and Proteomics Research

Discovery of New Knowledge by Using Information Embedded within

Families of Homologous Sequences and Their Structures

20

Protein FamilySuperfamily DefinitionsProtein FamilySuperfamily Definitions

Family A Set of Protein Sequences That Share a Common

Evolutionary Ancestor with End-to-End Sequence Similarity (No Major Discrepancy by Standard Multiple Alignment Methods)

Have the Same Domain Architecture (Except Incomplete or Alternately Spliced)

Overall Sequence Identity gt=45

Superfamily A Set of Protein Families That Share a Common Evolutionary

Ancestor From End-to-end Have the Same Domain Architecture Overall Sequence Identity gt=20

21

Protein Domain DefinitionProtein Domain Definition

Homology Domain A Recognizable Region of Similarity Have a Common Ancestry Found in Diverse Protein Sequences (in gt= 2 Superfamilies)

A Sequence Can Belong to Only One Protein Family and Superfamily but May Contain More Than One Domains

22

Superfamily-Domain-Motif RelationshipSuperfamily-Domain-Motif Relationship

23

iProClass Superfamily ListiProClass Superfamily ListAll Superfamilies Containing PF00001

Superfamily-Domain Relationship ~6000 SFs have gt=1 DomainsSuperfamily for Domain Architecture

24

iProClass Superfamily ReportiProClass Superfamily Report

25

Alignment and Tree ViewAlignment and Tree View

26

PIR-Protein Sequence DatabasePIR-Protein Sequence Database

27

PIR-PSD EntryPIR-PSD Entry

28

BLASTFASTA SearchBLASTFASTA Search

29

PIR FASTA Search ResultPIR FASTA Search Result

30

PIR Searches and AligmentPIR Searches and Aligment BLAST Search

Multiple Alignment amp Tree View

31

PIR Hidden Markov ModelPIR Hidden Markov Modelhttppirgeorgetownedupirwwwsearchpirhmmhtml

HMM Model Building amp Sequence Search

One Protein Against All HMMs

All Proteins Against One HMM

33

Bibliography SubmissionBibliography Submission

View Bibliography Information

View Protein Entry

Submit Citation with Optional Categorization

S1

34

Bibliography Information Display (I)Bibliography Information Display (I)

From PIR-NREF

From Other Curated Database (eg SGD)

35

Bibliography Information Display (II)Bibliography Information Display (II)

From User Submission

From Computer-Mapping (eg Gene Symbol)

36

Oracle DemoOracle DemoJava Web Interface for Oracle Database Search (httppirgeorgetowneduiproclasshtml)

WebDB Interface to Oracle (WebDB) TablesViewsObjects FunctionsProceduresPackages

37

Proteomic BioinformaticsProteomic Bioinformatics

Large-Scale Analysis of Proteomic Data Homology Search for Pathways

• Database Demo
• PIR Web Site (httppirgeorgetownedu)
• Text Search Result with NULLNOT NULL
• Peptide Search Results
• PIR-NREF Search Result (I)
• PIR-NREF Search Result (II)
• PIR Pattern Search
• PIR Pattern Search Result (I)
• PIR Pattern Search Result (II)
• PIR Domain Display
• PIR-NREF Database (httppirgeorgetownedupirwwwsearchpirnrefshtml)
• PIR-NREF Report
• PIR-iProClass Database
• iProClass Sequence Report
• PDB Structure of Molecule Inosine-5-Monophosphate Dehydrogenase
• Related Sequences
• Protein Family Classification
• Protein FamilySuperfamily Definitions
• Protein Domain Definition
• Superfamily-Domain-Motif Relationship
• iProClass Superfamily List
• iProClass Superfamily Report
• Alignment and Tree View
• PIR-Protein Sequence Database
• PIR-PSD Entry
• BLASTFASTA Search
• PIR FASTA Search Result
• PIR Searches and Aligment
• PIR Hidden Markov Model
• Bibliography Submission
• Bibliography Information Display (I)
• Bibliography Information Display (II)
• Oracle Demo
• Proteomic Bioinformatics

16

iProClass Sequence ReportiProClass Sequence Report

17

PDB Structure of Molecule Inosine-PDB Structure of Molecule Inosine-5-Monophosphate Dehydrogenase5-Monophosphate Dehydrogenase

18

Related Sequences Related Sequences

19

Protein Family ClassificationProtein Family Classification

Superfamily Domain and Motif ClassificationSuperfamily Concept End-to-End Similarity amp Same Overall Domain Architecture

Significance Improve Sensitivity of Protein Identification Provide Complete Clustering for Database Organization Detect and Correct Genome Annotation Errors Systematically Drive Other Annotations Stimulate Evolution Genomics and Proteomics Research

Discovery of New Knowledge by Using Information Embedded within

Families of Homologous Sequences and Their Structures

20

Protein FamilySuperfamily DefinitionsProtein FamilySuperfamily Definitions

Family A Set of Protein Sequences That Share a Common

Evolutionary Ancestor with End-to-End Sequence Similarity (No Major Discrepancy by Standard Multiple Alignment Methods)

Have the Same Domain Architecture (Except Incomplete or Alternately Spliced)

Overall Sequence Identity gt=45

Superfamily A Set of Protein Families That Share a Common Evolutionary

Ancestor From End-to-end Have the Same Domain Architecture Overall Sequence Identity gt=20

21

Protein Domain DefinitionProtein Domain Definition

Homology Domain A Recognizable Region of Similarity Have a Common Ancestry Found in Diverse Protein Sequences (in gt= 2 Superfamilies)

A Sequence Can Belong to Only One Protein Family and Superfamily but May Contain More Than One Domains

22

Superfamily-Domain-Motif RelationshipSuperfamily-Domain-Motif Relationship

23

iProClass Superfamily ListiProClass Superfamily ListAll Superfamilies Containing PF00001

Superfamily-Domain Relationship ~6000 SFs have gt=1 DomainsSuperfamily for Domain Architecture

24

iProClass Superfamily ReportiProClass Superfamily Report

25

Alignment and Tree ViewAlignment and Tree View

26

PIR-Protein Sequence DatabasePIR-Protein Sequence Database

27

PIR-PSD EntryPIR-PSD Entry

28

BLASTFASTA SearchBLASTFASTA Search

29

PIR FASTA Search ResultPIR FASTA Search Result

30

PIR Searches and AligmentPIR Searches and Aligment BLAST Search

Multiple Alignment amp Tree View

31

PIR Hidden Markov ModelPIR Hidden Markov Modelhttppirgeorgetownedupirwwwsearchpirhmmhtml

HMM Model Building amp Sequence Search

One Protein Against All HMMs

All Proteins Against One HMM

33

Bibliography SubmissionBibliography Submission

View Bibliography Information

View Protein Entry

Submit Citation with Optional Categorization

S1

34

Bibliography Information Display (I)Bibliography Information Display (I)

From PIR-NREF

From Other Curated Database (eg SGD)

35

Bibliography Information Display (II)Bibliography Information Display (II)

From User Submission

From Computer-Mapping (eg Gene Symbol)

36

Oracle DemoOracle DemoJava Web Interface for Oracle Database Search (httppirgeorgetowneduiproclasshtml)

WebDB Interface to Oracle (WebDB) TablesViewsObjects FunctionsProceduresPackages

37

Proteomic BioinformaticsProteomic Bioinformatics

Large-Scale Analysis of Proteomic Data Homology Search for Pathways

• Database Demo
• PIR Web Site (httppirgeorgetownedu)
• Text Search Result with NULLNOT NULL
• Peptide Search Results
• PIR-NREF Search Result (I)
• PIR-NREF Search Result (II)
• PIR Pattern Search
• PIR Pattern Search Result (I)
• PIR Pattern Search Result (II)
• PIR Domain Display
• PIR-NREF Database (httppirgeorgetownedupirwwwsearchpirnrefshtml)
• PIR-NREF Report
• PIR-iProClass Database
• iProClass Sequence Report
• PDB Structure of Molecule Inosine-5-Monophosphate Dehydrogenase
• Related Sequences
• Protein Family Classification
• Protein FamilySuperfamily Definitions
• Protein Domain Definition
• Superfamily-Domain-Motif Relationship
• iProClass Superfamily List
• iProClass Superfamily Report
• Alignment and Tree View
• PIR-Protein Sequence Database
• PIR-PSD Entry
• BLASTFASTA Search
• PIR FASTA Search Result
• PIR Searches and Aligment
• PIR Hidden Markov Model
• Bibliography Submission
• Bibliography Information Display (I)
• Bibliography Information Display (II)
• Oracle Demo
• Proteomic Bioinformatics

17

PDB Structure of Molecule Inosine-PDB Structure of Molecule Inosine-5-Monophosphate Dehydrogenase5-Monophosphate Dehydrogenase

18

Related Sequences Related Sequences

19

Protein Family ClassificationProtein Family Classification

Superfamily Domain and Motif ClassificationSuperfamily Concept End-to-End Similarity amp Same Overall Domain Architecture

Significance Improve Sensitivity of Protein Identification Provide Complete Clustering for Database Organization Detect and Correct Genome Annotation Errors Systematically Drive Other Annotations Stimulate Evolution Genomics and Proteomics Research

Discovery of New Knowledge by Using Information Embedded within

Families of Homologous Sequences and Their Structures

20

Protein FamilySuperfamily DefinitionsProtein FamilySuperfamily Definitions

Family A Set of Protein Sequences That Share a Common

Evolutionary Ancestor with End-to-End Sequence Similarity (No Major Discrepancy by Standard Multiple Alignment Methods)

Have the Same Domain Architecture (Except Incomplete or Alternately Spliced)

Overall Sequence Identity gt=45

Superfamily A Set of Protein Families That Share a Common Evolutionary

Ancestor From End-to-end Have the Same Domain Architecture Overall Sequence Identity gt=20

21

Protein Domain DefinitionProtein Domain Definition

Homology Domain A Recognizable Region of Similarity Have a Common Ancestry Found in Diverse Protein Sequences (in gt= 2 Superfamilies)

A Sequence Can Belong to Only One Protein Family and Superfamily but May Contain More Than One Domains

22

Superfamily-Domain-Motif RelationshipSuperfamily-Domain-Motif Relationship

23

iProClass Superfamily ListiProClass Superfamily ListAll Superfamilies Containing PF00001

Superfamily-Domain Relationship ~6000 SFs have gt=1 DomainsSuperfamily for Domain Architecture

24

iProClass Superfamily ReportiProClass Superfamily Report

25

Alignment and Tree ViewAlignment and Tree View

26

PIR-Protein Sequence DatabasePIR-Protein Sequence Database

27

PIR-PSD EntryPIR-PSD Entry

28

BLASTFASTA SearchBLASTFASTA Search

29

PIR FASTA Search ResultPIR FASTA Search Result

30

PIR Searches and AligmentPIR Searches and Aligment BLAST Search

Multiple Alignment amp Tree View

31

PIR Hidden Markov ModelPIR Hidden Markov Modelhttppirgeorgetownedupirwwwsearchpirhmmhtml

HMM Model Building amp Sequence Search

One Protein Against All HMMs

All Proteins Against One HMM

33

Bibliography SubmissionBibliography Submission

View Bibliography Information

View Protein Entry

Submit Citation with Optional Categorization

S1

34

Bibliography Information Display (I)Bibliography Information Display (I)

From PIR-NREF

From Other Curated Database (eg SGD)

35

Bibliography Information Display (II)Bibliography Information Display (II)

From User Submission

From Computer-Mapping (eg Gene Symbol)

36

Oracle DemoOracle DemoJava Web Interface for Oracle Database Search (httppirgeorgetowneduiproclasshtml)

WebDB Interface to Oracle (WebDB) TablesViewsObjects FunctionsProceduresPackages

37

Proteomic BioinformaticsProteomic Bioinformatics

Large-Scale Analysis of Proteomic Data Homology Search for Pathways

• Database Demo
• PIR Web Site (httppirgeorgetownedu)
• Text Search Result with NULLNOT NULL
• Peptide Search Results
• PIR-NREF Search Result (I)
• PIR-NREF Search Result (II)
• PIR Pattern Search
• PIR Pattern Search Result (I)
• PIR Pattern Search Result (II)
• PIR Domain Display
• PIR-NREF Database (httppirgeorgetownedupirwwwsearchpirnrefshtml)
• PIR-NREF Report
• PIR-iProClass Database
• iProClass Sequence Report
• PDB Structure of Molecule Inosine-5-Monophosphate Dehydrogenase
• Related Sequences
• Protein Family Classification
• Protein FamilySuperfamily Definitions
• Protein Domain Definition
• Superfamily-Domain-Motif Relationship
• iProClass Superfamily List
• iProClass Superfamily Report
• Alignment and Tree View
• PIR-Protein Sequence Database
• PIR-PSD Entry
• BLASTFASTA Search
• PIR FASTA Search Result
• PIR Searches and Aligment
• PIR Hidden Markov Model
• Bibliography Submission
• Bibliography Information Display (I)
• Bibliography Information Display (II)
• Oracle Demo
• Proteomic Bioinformatics

18

Related Sequences Related Sequences

19

Protein Family ClassificationProtein Family Classification

Superfamily Domain and Motif ClassificationSuperfamily Concept End-to-End Similarity amp Same Overall Domain Architecture

Significance Improve Sensitivity of Protein Identification Provide Complete Clustering for Database Organization Detect and Correct Genome Annotation Errors Systematically Drive Other Annotations Stimulate Evolution Genomics and Proteomics Research

Discovery of New Knowledge by Using Information Embedded within

Families of Homologous Sequences and Their Structures

20

Protein FamilySuperfamily DefinitionsProtein FamilySuperfamily Definitions

Family A Set of Protein Sequences That Share a Common

Evolutionary Ancestor with End-to-End Sequence Similarity (No Major Discrepancy by Standard Multiple Alignment Methods)

Have the Same Domain Architecture (Except Incomplete or Alternately Spliced)

Overall Sequence Identity gt=45

Superfamily A Set of Protein Families That Share a Common Evolutionary

Ancestor From End-to-end Have the Same Domain Architecture Overall Sequence Identity gt=20

21

Protein Domain DefinitionProtein Domain Definition

Homology Domain A Recognizable Region of Similarity Have a Common Ancestry Found in Diverse Protein Sequences (in gt= 2 Superfamilies)

A Sequence Can Belong to Only One Protein Family and Superfamily but May Contain More Than One Domains

22

Superfamily-Domain-Motif RelationshipSuperfamily-Domain-Motif Relationship

23

iProClass Superfamily ListiProClass Superfamily ListAll Superfamilies Containing PF00001

Superfamily-Domain Relationship ~6000 SFs have gt=1 DomainsSuperfamily for Domain Architecture

24

iProClass Superfamily ReportiProClass Superfamily Report

25

Alignment and Tree ViewAlignment and Tree View

26

PIR-Protein Sequence DatabasePIR-Protein Sequence Database

27

PIR-PSD EntryPIR-PSD Entry

28

BLASTFASTA SearchBLASTFASTA Search

29

PIR FASTA Search ResultPIR FASTA Search Result

30

PIR Searches and AligmentPIR Searches and Aligment BLAST Search

Multiple Alignment amp Tree View

31

PIR Hidden Markov ModelPIR Hidden Markov Modelhttppirgeorgetownedupirwwwsearchpirhmmhtml

HMM Model Building amp Sequence Search

One Protein Against All HMMs

All Proteins Against One HMM

33

Bibliography SubmissionBibliography Submission

View Bibliography Information

View Protein Entry

Submit Citation with Optional Categorization

S1

34

Bibliography Information Display (I)Bibliography Information Display (I)

From PIR-NREF

From Other Curated Database (eg SGD)

35

Bibliography Information Display (II)Bibliography Information Display (II)

From User Submission

From Computer-Mapping (eg Gene Symbol)

36

Oracle DemoOracle DemoJava Web Interface for Oracle Database Search (httppirgeorgetowneduiproclasshtml)

WebDB Interface to Oracle (WebDB) TablesViewsObjects FunctionsProceduresPackages

37

Proteomic BioinformaticsProteomic Bioinformatics

Large-Scale Analysis of Proteomic Data Homology Search for Pathways

• Database Demo
• PIR Web Site (httppirgeorgetownedu)
• Text Search Result with NULLNOT NULL
• Peptide Search Results
• PIR-NREF Search Result (I)
• PIR-NREF Search Result (II)
• PIR Pattern Search
• PIR Pattern Search Result (I)
• PIR Pattern Search Result (II)
• PIR Domain Display
• PIR-NREF Database (httppirgeorgetownedupirwwwsearchpirnrefshtml)
• PIR-NREF Report
• PIR-iProClass Database
• iProClass Sequence Report
• PDB Structure of Molecule Inosine-5-Monophosphate Dehydrogenase
• Related Sequences
• Protein Family Classification
• Protein FamilySuperfamily Definitions
• Protein Domain Definition
• Superfamily-Domain-Motif Relationship
• iProClass Superfamily List
• iProClass Superfamily Report
• Alignment and Tree View
• PIR-Protein Sequence Database
• PIR-PSD Entry
• BLASTFASTA Search
• PIR FASTA Search Result
• PIR Searches and Aligment
• PIR Hidden Markov Model
• Bibliography Submission
• Bibliography Information Display (I)
• Bibliography Information Display (II)
• Oracle Demo
• Proteomic Bioinformatics

19

Protein Family ClassificationProtein Family Classification

Superfamily Domain and Motif ClassificationSuperfamily Concept End-to-End Similarity amp Same Overall Domain Architecture

Significance Improve Sensitivity of Protein Identification Provide Complete Clustering for Database Organization Detect and Correct Genome Annotation Errors Systematically Drive Other Annotations Stimulate Evolution Genomics and Proteomics Research

Discovery of New Knowledge by Using Information Embedded within

Families of Homologous Sequences and Their Structures

20

Protein FamilySuperfamily DefinitionsProtein FamilySuperfamily Definitions

Family A Set of Protein Sequences That Share a Common

Evolutionary Ancestor with End-to-End Sequence Similarity (No Major Discrepancy by Standard Multiple Alignment Methods)

Have the Same Domain Architecture (Except Incomplete or Alternately Spliced)

Overall Sequence Identity gt=45

Superfamily A Set of Protein Families That Share a Common Evolutionary

Ancestor From End-to-end Have the Same Domain Architecture Overall Sequence Identity gt=20

21

Protein Domain DefinitionProtein Domain Definition

Homology Domain A Recognizable Region of Similarity Have a Common Ancestry Found in Diverse Protein Sequences (in gt= 2 Superfamilies)

A Sequence Can Belong to Only One Protein Family and Superfamily but May Contain More Than One Domains

22

Superfamily-Domain-Motif RelationshipSuperfamily-Domain-Motif Relationship

23

iProClass Superfamily ListiProClass Superfamily ListAll Superfamilies Containing PF00001

Superfamily-Domain Relationship ~6000 SFs have gt=1 DomainsSuperfamily for Domain Architecture

24

iProClass Superfamily ReportiProClass Superfamily Report

25

Alignment and Tree ViewAlignment and Tree View

26

PIR-Protein Sequence DatabasePIR-Protein Sequence Database

27

PIR-PSD EntryPIR-PSD Entry

28

BLASTFASTA SearchBLASTFASTA Search

29

PIR FASTA Search ResultPIR FASTA Search Result

30

PIR Searches and AligmentPIR Searches and Aligment BLAST Search

Multiple Alignment amp Tree View

31

PIR Hidden Markov ModelPIR Hidden Markov Modelhttppirgeorgetownedupirwwwsearchpirhmmhtml

HMM Model Building amp Sequence Search

One Protein Against All HMMs

All Proteins Against One HMM

33

Bibliography SubmissionBibliography Submission

View Bibliography Information

View Protein Entry

Submit Citation with Optional Categorization

S1

34

Bibliography Information Display (I)Bibliography Information Display (I)

From PIR-NREF

From Other Curated Database (eg SGD)

35

Bibliography Information Display (II)Bibliography Information Display (II)

From User Submission

From Computer-Mapping (eg Gene Symbol)

36

Oracle DemoOracle DemoJava Web Interface for Oracle Database Search (httppirgeorgetowneduiproclasshtml)

WebDB Interface to Oracle (WebDB) TablesViewsObjects FunctionsProceduresPackages

37

Proteomic BioinformaticsProteomic Bioinformatics

Large-Scale Analysis of Proteomic Data Homology Search for Pathways

• Database Demo
• PIR Web Site (httppirgeorgetownedu)
• Text Search Result with NULLNOT NULL
• Peptide Search Results
• PIR-NREF Search Result (I)
• PIR-NREF Search Result (II)
• PIR Pattern Search
• PIR Pattern Search Result (I)
• PIR Pattern Search Result (II)
• PIR Domain Display
• PIR-NREF Database (httppirgeorgetownedupirwwwsearchpirnrefshtml)
• PIR-NREF Report
• PIR-iProClass Database
• iProClass Sequence Report
• PDB Structure of Molecule Inosine-5-Monophosphate Dehydrogenase
• Related Sequences
• Protein Family Classification
• Protein FamilySuperfamily Definitions
• Protein Domain Definition
• Superfamily-Domain-Motif Relationship
• iProClass Superfamily List
• iProClass Superfamily Report
• Alignment and Tree View
• PIR-Protein Sequence Database
• PIR-PSD Entry
• BLASTFASTA Search
• PIR FASTA Search Result
• PIR Searches and Aligment
• PIR Hidden Markov Model
• Bibliography Submission
• Bibliography Information Display (I)
• Bibliography Information Display (II)
• Oracle Demo
• Proteomic Bioinformatics

20

Protein FamilySuperfamily DefinitionsProtein FamilySuperfamily Definitions

Family A Set of Protein Sequences That Share a Common

Evolutionary Ancestor with End-to-End Sequence Similarity (No Major Discrepancy by Standard Multiple Alignment Methods)

Have the Same Domain Architecture (Except Incomplete or Alternately Spliced)

Overall Sequence Identity gt=45

Superfamily A Set of Protein Families That Share a Common Evolutionary

Ancestor From End-to-end Have the Same Domain Architecture Overall Sequence Identity gt=20

21

Protein Domain DefinitionProtein Domain Definition

Homology Domain A Recognizable Region of Similarity Have a Common Ancestry Found in Diverse Protein Sequences (in gt= 2 Superfamilies)

A Sequence Can Belong to Only One Protein Family and Superfamily but May Contain More Than One Domains

22

Superfamily-Domain-Motif RelationshipSuperfamily-Domain-Motif Relationship

23

iProClass Superfamily ListiProClass Superfamily ListAll Superfamilies Containing PF00001

Superfamily-Domain Relationship ~6000 SFs have gt=1 DomainsSuperfamily for Domain Architecture

24

iProClass Superfamily ReportiProClass Superfamily Report

25

Alignment and Tree ViewAlignment and Tree View

26

PIR-Protein Sequence DatabasePIR-Protein Sequence Database

27

PIR-PSD EntryPIR-PSD Entry

28

BLASTFASTA SearchBLASTFASTA Search

29

PIR FASTA Search ResultPIR FASTA Search Result

30

PIR Searches and AligmentPIR Searches and Aligment BLAST Search

Multiple Alignment amp Tree View

31

PIR Hidden Markov ModelPIR Hidden Markov Modelhttppirgeorgetownedupirwwwsearchpirhmmhtml

HMM Model Building amp Sequence Search

One Protein Against All HMMs

All Proteins Against One HMM

33

Bibliography SubmissionBibliography Submission

View Bibliography Information

View Protein Entry

Submit Citation with Optional Categorization

S1

34

Bibliography Information Display (I)Bibliography Information Display (I)

From PIR-NREF

From Other Curated Database (eg SGD)

35

Bibliography Information Display (II)Bibliography Information Display (II)

From User Submission

From Computer-Mapping (eg Gene Symbol)

36

Oracle DemoOracle DemoJava Web Interface for Oracle Database Search (httppirgeorgetowneduiproclasshtml)

WebDB Interface to Oracle (WebDB) TablesViewsObjects FunctionsProceduresPackages

37

Proteomic BioinformaticsProteomic Bioinformatics

Large-Scale Analysis of Proteomic Data Homology Search for Pathways

• Database Demo
• PIR Web Site (httppirgeorgetownedu)
• Text Search Result with NULLNOT NULL
• Peptide Search Results
• PIR-NREF Search Result (I)
• PIR-NREF Search Result (II)
• PIR Pattern Search
• PIR Pattern Search Result (I)
• PIR Pattern Search Result (II)
• PIR Domain Display
• PIR-NREF Database (httppirgeorgetownedupirwwwsearchpirnrefshtml)
• PIR-NREF Report
• PIR-iProClass Database
• iProClass Sequence Report
• PDB Structure of Molecule Inosine-5-Monophosphate Dehydrogenase
• Related Sequences
• Protein Family Classification
• Protein FamilySuperfamily Definitions
• Protein Domain Definition
• Superfamily-Domain-Motif Relationship
• iProClass Superfamily List
• iProClass Superfamily Report
• Alignment and Tree View
• PIR-Protein Sequence Database
• PIR-PSD Entry
• BLASTFASTA Search
• PIR FASTA Search Result
• PIR Searches and Aligment
• PIR Hidden Markov Model
• Bibliography Submission
• Bibliography Information Display (I)
• Bibliography Information Display (II)
• Oracle Demo
• Proteomic Bioinformatics

21

Protein Domain DefinitionProtein Domain Definition

Homology Domain A Recognizable Region of Similarity Have a Common Ancestry Found in Diverse Protein Sequences (in gt= 2 Superfamilies)

A Sequence Can Belong to Only One Protein Family and Superfamily but May Contain More Than One Domains

22

Superfamily-Domain-Motif RelationshipSuperfamily-Domain-Motif Relationship

23

iProClass Superfamily ListiProClass Superfamily ListAll Superfamilies Containing PF00001

Superfamily-Domain Relationship ~6000 SFs have gt=1 DomainsSuperfamily for Domain Architecture

24

iProClass Superfamily ReportiProClass Superfamily Report

25

Alignment and Tree ViewAlignment and Tree View

26

PIR-Protein Sequence DatabasePIR-Protein Sequence Database

27

PIR-PSD EntryPIR-PSD Entry

28

BLASTFASTA SearchBLASTFASTA Search

29

PIR FASTA Search ResultPIR FASTA Search Result

30

PIR Searches and AligmentPIR Searches and Aligment BLAST Search

Multiple Alignment amp Tree View

31

PIR Hidden Markov ModelPIR Hidden Markov Modelhttppirgeorgetownedupirwwwsearchpirhmmhtml

HMM Model Building amp Sequence Search

One Protein Against All HMMs

All Proteins Against One HMM

33

Bibliography SubmissionBibliography Submission

View Bibliography Information

View Protein Entry

Submit Citation with Optional Categorization

S1

34

Bibliography Information Display (I)Bibliography Information Display (I)

From PIR-NREF

From Other Curated Database (eg SGD)

35

Bibliography Information Display (II)Bibliography Information Display (II)

From User Submission

From Computer-Mapping (eg Gene Symbol)

36

Oracle DemoOracle DemoJava Web Interface for Oracle Database Search (httppirgeorgetowneduiproclasshtml)

WebDB Interface to Oracle (WebDB) TablesViewsObjects FunctionsProceduresPackages

37

Proteomic BioinformaticsProteomic Bioinformatics

Large-Scale Analysis of Proteomic Data Homology Search for Pathways

• Database Demo
• PIR Web Site (httppirgeorgetownedu)
• Text Search Result with NULLNOT NULL
• Peptide Search Results
• PIR-NREF Search Result (I)
• PIR-NREF Search Result (II)
• PIR Pattern Search
• PIR Pattern Search Result (I)
• PIR Pattern Search Result (II)
• PIR Domain Display
• PIR-NREF Database (httppirgeorgetownedupirwwwsearchpirnrefshtml)
• PIR-NREF Report
• PIR-iProClass Database
• iProClass Sequence Report
• PDB Structure of Molecule Inosine-5-Monophosphate Dehydrogenase
• Related Sequences
• Protein Family Classification
• Protein FamilySuperfamily Definitions
• Protein Domain Definition
• Superfamily-Domain-Motif Relationship
• iProClass Superfamily List
• iProClass Superfamily Report
• Alignment and Tree View
• PIR-Protein Sequence Database
• PIR-PSD Entry
• BLASTFASTA Search
• PIR FASTA Search Result
• PIR Searches and Aligment
• PIR Hidden Markov Model
• Bibliography Submission
• Bibliography Information Display (I)
• Bibliography Information Display (II)
• Oracle Demo
• Proteomic Bioinformatics

22

Superfamily-Domain-Motif RelationshipSuperfamily-Domain-Motif Relationship

23

iProClass Superfamily ListiProClass Superfamily ListAll Superfamilies Containing PF00001

Superfamily-Domain Relationship ~6000 SFs have gt=1 DomainsSuperfamily for Domain Architecture

24

iProClass Superfamily ReportiProClass Superfamily Report

25

Alignment and Tree ViewAlignment and Tree View

26

PIR-Protein Sequence DatabasePIR-Protein Sequence Database

27

PIR-PSD EntryPIR-PSD Entry

28

BLASTFASTA SearchBLASTFASTA Search

29

PIR FASTA Search ResultPIR FASTA Search Result

30

PIR Searches and AligmentPIR Searches and Aligment BLAST Search

Multiple Alignment amp Tree View

31

PIR Hidden Markov ModelPIR Hidden Markov Modelhttppirgeorgetownedupirwwwsearchpirhmmhtml

HMM Model Building amp Sequence Search

One Protein Against All HMMs

All Proteins Against One HMM

33

Bibliography SubmissionBibliography Submission

View Bibliography Information

View Protein Entry

Submit Citation with Optional Categorization

S1

34

Bibliography Information Display (I)Bibliography Information Display (I)

From PIR-NREF

From Other Curated Database (eg SGD)

35

Bibliography Information Display (II)Bibliography Information Display (II)

From User Submission

From Computer-Mapping (eg Gene Symbol)

36

Oracle DemoOracle DemoJava Web Interface for Oracle Database Search (httppirgeorgetowneduiproclasshtml)

WebDB Interface to Oracle (WebDB) TablesViewsObjects FunctionsProceduresPackages

37

Proteomic BioinformaticsProteomic Bioinformatics

Large-Scale Analysis of Proteomic Data Homology Search for Pathways

• Database Demo
• PIR Web Site (httppirgeorgetownedu)
• Text Search Result with NULLNOT NULL
• Peptide Search Results
• PIR-NREF Search Result (I)
• PIR-NREF Search Result (II)
• PIR Pattern Search
• PIR Pattern Search Result (I)
• PIR Pattern Search Result (II)
• PIR Domain Display
• PIR-NREF Database (httppirgeorgetownedupirwwwsearchpirnrefshtml)
• PIR-NREF Report
• PIR-iProClass Database
• iProClass Sequence Report
• PDB Structure of Molecule Inosine-5-Monophosphate Dehydrogenase
• Related Sequences
• Protein Family Classification
• Protein FamilySuperfamily Definitions
• Protein Domain Definition
• Superfamily-Domain-Motif Relationship
• iProClass Superfamily List
• iProClass Superfamily Report
• Alignment and Tree View
• PIR-Protein Sequence Database
• PIR-PSD Entry
• BLASTFASTA Search
• PIR FASTA Search Result
• PIR Searches and Aligment
• PIR Hidden Markov Model
• Bibliography Submission
• Bibliography Information Display (I)
• Bibliography Information Display (II)
• Oracle Demo
• Proteomic Bioinformatics

23

iProClass Superfamily ListiProClass Superfamily ListAll Superfamilies Containing PF00001

Superfamily-Domain Relationship ~6000 SFs have gt=1 DomainsSuperfamily for Domain Architecture

24

iProClass Superfamily ReportiProClass Superfamily Report

25

Alignment and Tree ViewAlignment and Tree View

26

PIR-Protein Sequence DatabasePIR-Protein Sequence Database

27

PIR-PSD EntryPIR-PSD Entry

28

BLASTFASTA SearchBLASTFASTA Search

29

PIR FASTA Search ResultPIR FASTA Search Result

30

PIR Searches and AligmentPIR Searches and Aligment BLAST Search

Multiple Alignment amp Tree View

31

PIR Hidden Markov ModelPIR Hidden Markov Modelhttppirgeorgetownedupirwwwsearchpirhmmhtml

HMM Model Building amp Sequence Search

One Protein Against All HMMs

All Proteins Against One HMM

33

Bibliography SubmissionBibliography Submission

View Bibliography Information

View Protein Entry

Submit Citation with Optional Categorization

S1

34

Bibliography Information Display (I)Bibliography Information Display (I)

From PIR-NREF

From Other Curated Database (eg SGD)

35

Bibliography Information Display (II)Bibliography Information Display (II)

From User Submission

From Computer-Mapping (eg Gene Symbol)

36

Oracle DemoOracle DemoJava Web Interface for Oracle Database Search (httppirgeorgetowneduiproclasshtml)

WebDB Interface to Oracle (WebDB) TablesViewsObjects FunctionsProceduresPackages

37

Proteomic BioinformaticsProteomic Bioinformatics

Large-Scale Analysis of Proteomic Data Homology Search for Pathways

• Database Demo
• PIR Web Site (httppirgeorgetownedu)
• Text Search Result with NULLNOT NULL
• Peptide Search Results
• PIR-NREF Search Result (I)
• PIR-NREF Search Result (II)
• PIR Pattern Search
• PIR Pattern Search Result (I)
• PIR Pattern Search Result (II)
• PIR Domain Display
• PIR-NREF Database (httppirgeorgetownedupirwwwsearchpirnrefshtml)
• PIR-NREF Report
• PIR-iProClass Database
• iProClass Sequence Report
• PDB Structure of Molecule Inosine-5-Monophosphate Dehydrogenase
• Related Sequences
• Protein Family Classification
• Protein FamilySuperfamily Definitions
• Protein Domain Definition
• Superfamily-Domain-Motif Relationship
• iProClass Superfamily List
• iProClass Superfamily Report
• Alignment and Tree View
• PIR-Protein Sequence Database
• PIR-PSD Entry
• BLASTFASTA Search
• PIR FASTA Search Result
• PIR Searches and Aligment
• PIR Hidden Markov Model
• Bibliography Submission
• Bibliography Information Display (I)
• Bibliography Information Display (II)
• Oracle Demo
• Proteomic Bioinformatics

24

iProClass Superfamily ReportiProClass Superfamily Report

25

Alignment and Tree ViewAlignment and Tree View

26

PIR-Protein Sequence DatabasePIR-Protein Sequence Database

27

PIR-PSD EntryPIR-PSD Entry

28

BLASTFASTA SearchBLASTFASTA Search

29

PIR FASTA Search ResultPIR FASTA Search Result

30

PIR Searches and AligmentPIR Searches and Aligment BLAST Search

Multiple Alignment amp Tree View

31

PIR Hidden Markov ModelPIR Hidden Markov Modelhttppirgeorgetownedupirwwwsearchpirhmmhtml

HMM Model Building amp Sequence Search

One Protein Against All HMMs

All Proteins Against One HMM

33

Bibliography SubmissionBibliography Submission

View Bibliography Information

View Protein Entry

Submit Citation with Optional Categorization

S1

34

Bibliography Information Display (I)Bibliography Information Display (I)

From PIR-NREF

From Other Curated Database (eg SGD)

35

Bibliography Information Display (II)Bibliography Information Display (II)

From User Submission

From Computer-Mapping (eg Gene Symbol)

36

Oracle DemoOracle DemoJava Web Interface for Oracle Database Search (httppirgeorgetowneduiproclasshtml)

WebDB Interface to Oracle (WebDB) TablesViewsObjects FunctionsProceduresPackages

37

Proteomic BioinformaticsProteomic Bioinformatics

Large-Scale Analysis of Proteomic Data Homology Search for Pathways

• Database Demo
• PIR Web Site (httppirgeorgetownedu)
• Text Search Result with NULLNOT NULL
• Peptide Search Results
• PIR-NREF Search Result (I)
• PIR-NREF Search Result (II)
• PIR Pattern Search
• PIR Pattern Search Result (I)
• PIR Pattern Search Result (II)
• PIR Domain Display
• PIR-NREF Database (httppirgeorgetownedupirwwwsearchpirnrefshtml)
• PIR-NREF Report
• PIR-iProClass Database
• iProClass Sequence Report
• PDB Structure of Molecule Inosine-5-Monophosphate Dehydrogenase
• Related Sequences
• Protein Family Classification
• Protein FamilySuperfamily Definitions
• Protein Domain Definition
• Superfamily-Domain-Motif Relationship
• iProClass Superfamily List
• iProClass Superfamily Report
• Alignment and Tree View
• PIR-Protein Sequence Database
• PIR-PSD Entry
• BLASTFASTA Search
• PIR FASTA Search Result
• PIR Searches and Aligment
• PIR Hidden Markov Model
• Bibliography Submission
• Bibliography Information Display (I)
• Bibliography Information Display (II)
• Oracle Demo
• Proteomic Bioinformatics

25

Alignment and Tree ViewAlignment and Tree View

26

PIR-Protein Sequence DatabasePIR-Protein Sequence Database

27

PIR-PSD EntryPIR-PSD Entry

28

BLASTFASTA SearchBLASTFASTA Search

29

PIR FASTA Search ResultPIR FASTA Search Result

30

PIR Searches and AligmentPIR Searches and Aligment BLAST Search

Multiple Alignment amp Tree View

31

PIR Hidden Markov ModelPIR Hidden Markov Modelhttppirgeorgetownedupirwwwsearchpirhmmhtml

HMM Model Building amp Sequence Search

One Protein Against All HMMs

All Proteins Against One HMM

33

Bibliography SubmissionBibliography Submission

View Bibliography Information

View Protein Entry

Submit Citation with Optional Categorization

S1

34

Bibliography Information Display (I)Bibliography Information Display (I)

From PIR-NREF

From Other Curated Database (eg SGD)

35

Bibliography Information Display (II)Bibliography Information Display (II)

From User Submission

From Computer-Mapping (eg Gene Symbol)

36

Oracle DemoOracle DemoJava Web Interface for Oracle Database Search (httppirgeorgetowneduiproclasshtml)

WebDB Interface to Oracle (WebDB) TablesViewsObjects FunctionsProceduresPackages

37

Proteomic BioinformaticsProteomic Bioinformatics

Large-Scale Analysis of Proteomic Data Homology Search for Pathways

• Database Demo
• PIR Web Site (httppirgeorgetownedu)
• Text Search Result with NULLNOT NULL
• Peptide Search Results
• PIR-NREF Search Result (I)
• PIR-NREF Search Result (II)
• PIR Pattern Search
• PIR Pattern Search Result (I)
• PIR Pattern Search Result (II)
• PIR Domain Display
• PIR-NREF Database (httppirgeorgetownedupirwwwsearchpirnrefshtml)
• PIR-NREF Report
• PIR-iProClass Database
• iProClass Sequence Report
• PDB Structure of Molecule Inosine-5-Monophosphate Dehydrogenase
• Related Sequences
• Protein Family Classification
• Protein FamilySuperfamily Definitions
• Protein Domain Definition
• Superfamily-Domain-Motif Relationship
• iProClass Superfamily List
• iProClass Superfamily Report
• Alignment and Tree View
• PIR-Protein Sequence Database
• PIR-PSD Entry
• BLASTFASTA Search
• PIR FASTA Search Result
• PIR Searches and Aligment
• PIR Hidden Markov Model
• Bibliography Submission
• Bibliography Information Display (I)
• Bibliography Information Display (II)
• Oracle Demo
• Proteomic Bioinformatics

26

PIR-Protein Sequence DatabasePIR-Protein Sequence Database

27

PIR-PSD EntryPIR-PSD Entry

28

BLASTFASTA SearchBLASTFASTA Search

29

PIR FASTA Search ResultPIR FASTA Search Result

30

PIR Searches and AligmentPIR Searches and Aligment BLAST Search

Multiple Alignment amp Tree View

31

PIR Hidden Markov ModelPIR Hidden Markov Modelhttppirgeorgetownedupirwwwsearchpirhmmhtml

HMM Model Building amp Sequence Search

One Protein Against All HMMs

All Proteins Against One HMM

33

Bibliography SubmissionBibliography Submission

View Bibliography Information

View Protein Entry

Submit Citation with Optional Categorization

S1

34

Bibliography Information Display (I)Bibliography Information Display (I)

From PIR-NREF

From Other Curated Database (eg SGD)

35

Bibliography Information Display (II)Bibliography Information Display (II)

From User Submission

From Computer-Mapping (eg Gene Symbol)

36

Oracle DemoOracle DemoJava Web Interface for Oracle Database Search (httppirgeorgetowneduiproclasshtml)

WebDB Interface to Oracle (WebDB) TablesViewsObjects FunctionsProceduresPackages

37

Proteomic BioinformaticsProteomic Bioinformatics

Large-Scale Analysis of Proteomic Data Homology Search for Pathways

• Database Demo
• PIR Web Site (httppirgeorgetownedu)
• Text Search Result with NULLNOT NULL
• Peptide Search Results
• PIR-NREF Search Result (I)
• PIR-NREF Search Result (II)
• PIR Pattern Search
• PIR Pattern Search Result (I)
• PIR Pattern Search Result (II)
• PIR Domain Display
• PIR-NREF Database (httppirgeorgetownedupirwwwsearchpirnrefshtml)
• PIR-NREF Report
• PIR-iProClass Database
• iProClass Sequence Report
• PDB Structure of Molecule Inosine-5-Monophosphate Dehydrogenase
• Related Sequences
• Protein Family Classification
• Protein FamilySuperfamily Definitions
• Protein Domain Definition
• Superfamily-Domain-Motif Relationship
• iProClass Superfamily List
• iProClass Superfamily Report
• Alignment and Tree View
• PIR-Protein Sequence Database
• PIR-PSD Entry
• BLASTFASTA Search
• PIR FASTA Search Result
• PIR Searches and Aligment
• PIR Hidden Markov Model
• Bibliography Submission
• Bibliography Information Display (I)
• Bibliography Information Display (II)
• Oracle Demo
• Proteomic Bioinformatics

27

PIR-PSD EntryPIR-PSD Entry

28

BLASTFASTA SearchBLASTFASTA Search

29

PIR FASTA Search ResultPIR FASTA Search Result

30

PIR Searches and AligmentPIR Searches and Aligment BLAST Search

Multiple Alignment amp Tree View

31

PIR Hidden Markov ModelPIR Hidden Markov Modelhttppirgeorgetownedupirwwwsearchpirhmmhtml

HMM Model Building amp Sequence Search

One Protein Against All HMMs

All Proteins Against One HMM

33

Bibliography SubmissionBibliography Submission

View Bibliography Information

View Protein Entry

Submit Citation with Optional Categorization

S1

34

Bibliography Information Display (I)Bibliography Information Display (I)

From PIR-NREF

From Other Curated Database (eg SGD)

35

Bibliography Information Display (II)Bibliography Information Display (II)

From User Submission

From Computer-Mapping (eg Gene Symbol)

36

Oracle DemoOracle DemoJava Web Interface for Oracle Database Search (httppirgeorgetowneduiproclasshtml)

WebDB Interface to Oracle (WebDB) TablesViewsObjects FunctionsProceduresPackages

37

Proteomic BioinformaticsProteomic Bioinformatics

Large-Scale Analysis of Proteomic Data Homology Search for Pathways

• Database Demo
• PIR Web Site (httppirgeorgetownedu)
• Text Search Result with NULLNOT NULL
• Peptide Search Results
• PIR-NREF Search Result (I)
• PIR-NREF Search Result (II)
• PIR Pattern Search
• PIR Pattern Search Result (I)
• PIR Pattern Search Result (II)
• PIR Domain Display
• PIR-NREF Database (httppirgeorgetownedupirwwwsearchpirnrefshtml)
• PIR-NREF Report
• PIR-iProClass Database
• iProClass Sequence Report
• PDB Structure of Molecule Inosine-5-Monophosphate Dehydrogenase
• Related Sequences
• Protein Family Classification
• Protein FamilySuperfamily Definitions
• Protein Domain Definition
• Superfamily-Domain-Motif Relationship
• iProClass Superfamily List
• iProClass Superfamily Report
• Alignment and Tree View
• PIR-Protein Sequence Database
• PIR-PSD Entry
• BLASTFASTA Search
• PIR FASTA Search Result
• PIR Searches and Aligment
• PIR Hidden Markov Model
• Bibliography Submission
• Bibliography Information Display (I)
• Bibliography Information Display (II)
• Oracle Demo
• Proteomic Bioinformatics

28

BLASTFASTA SearchBLASTFASTA Search

29

PIR FASTA Search ResultPIR FASTA Search Result

30

PIR Searches and AligmentPIR Searches and Aligment BLAST Search

Multiple Alignment amp Tree View

31

PIR Hidden Markov ModelPIR Hidden Markov Modelhttppirgeorgetownedupirwwwsearchpirhmmhtml

HMM Model Building amp Sequence Search

One Protein Against All HMMs

All Proteins Against One HMM

33

Bibliography SubmissionBibliography Submission

View Bibliography Information

View Protein Entry

Submit Citation with Optional Categorization

S1

34

Bibliography Information Display (I)Bibliography Information Display (I)

From PIR-NREF

From Other Curated Database (eg SGD)

35

Bibliography Information Display (II)Bibliography Information Display (II)

From User Submission

From Computer-Mapping (eg Gene Symbol)

36

Oracle DemoOracle DemoJava Web Interface for Oracle Database Search (httppirgeorgetowneduiproclasshtml)

WebDB Interface to Oracle (WebDB) TablesViewsObjects FunctionsProceduresPackages

37

Proteomic BioinformaticsProteomic Bioinformatics

Large-Scale Analysis of Proteomic Data Homology Search for Pathways

• Database Demo
• PIR Web Site (httppirgeorgetownedu)
• Text Search Result with NULLNOT NULL
• Peptide Search Results
• PIR-NREF Search Result (I)
• PIR-NREF Search Result (II)
• PIR Pattern Search
• PIR Pattern Search Result (I)
• PIR Pattern Search Result (II)
• PIR Domain Display
• PIR-NREF Database (httppirgeorgetownedupirwwwsearchpirnrefshtml)
• PIR-NREF Report
• PIR-iProClass Database
• iProClass Sequence Report
• PDB Structure of Molecule Inosine-5-Monophosphate Dehydrogenase
• Related Sequences
• Protein Family Classification
• Protein FamilySuperfamily Definitions
• Protein Domain Definition
• Superfamily-Domain-Motif Relationship
• iProClass Superfamily List
• iProClass Superfamily Report
• Alignment and Tree View
• PIR-Protein Sequence Database
• PIR-PSD Entry
• BLASTFASTA Search
• PIR FASTA Search Result
• PIR Searches and Aligment
• PIR Hidden Markov Model
• Bibliography Submission
• Bibliography Information Display (I)
• Bibliography Information Display (II)
• Oracle Demo
• Proteomic Bioinformatics

29

PIR FASTA Search ResultPIR FASTA Search Result

30

PIR Searches and AligmentPIR Searches and Aligment BLAST Search

Multiple Alignment amp Tree View

31

PIR Hidden Markov ModelPIR Hidden Markov Modelhttppirgeorgetownedupirwwwsearchpirhmmhtml

HMM Model Building amp Sequence Search

One Protein Against All HMMs

All Proteins Against One HMM

33

Bibliography SubmissionBibliography Submission

View Bibliography Information

View Protein Entry

Submit Citation with Optional Categorization

S1

34

Bibliography Information Display (I)Bibliography Information Display (I)

From PIR-NREF

From Other Curated Database (eg SGD)

35

Bibliography Information Display (II)Bibliography Information Display (II)

From User Submission

From Computer-Mapping (eg Gene Symbol)

36

Oracle DemoOracle DemoJava Web Interface for Oracle Database Search (httppirgeorgetowneduiproclasshtml)

WebDB Interface to Oracle (WebDB) TablesViewsObjects FunctionsProceduresPackages

37

Proteomic BioinformaticsProteomic Bioinformatics

Large-Scale Analysis of Proteomic Data Homology Search for Pathways

• Database Demo
• PIR Web Site (httppirgeorgetownedu)
• Text Search Result with NULLNOT NULL
• Peptide Search Results
• PIR-NREF Search Result (I)
• PIR-NREF Search Result (II)
• PIR Pattern Search
• PIR Pattern Search Result (I)
• PIR Pattern Search Result (II)
• PIR Domain Display
• PIR-NREF Database (httppirgeorgetownedupirwwwsearchpirnrefshtml)
• PIR-NREF Report
• PIR-iProClass Database
• iProClass Sequence Report
• PDB Structure of Molecule Inosine-5-Monophosphate Dehydrogenase
• Related Sequences
• Protein Family Classification
• Protein FamilySuperfamily Definitions
• Protein Domain Definition
• Superfamily-Domain-Motif Relationship
• iProClass Superfamily List
• iProClass Superfamily Report
• Alignment and Tree View
• PIR-Protein Sequence Database
• PIR-PSD Entry
• BLASTFASTA Search
• PIR FASTA Search Result
• PIR Searches and Aligment
• PIR Hidden Markov Model
• Bibliography Submission
• Bibliography Information Display (I)
• Bibliography Information Display (II)
• Oracle Demo
• Proteomic Bioinformatics

30

PIR Searches and AligmentPIR Searches and Aligment BLAST Search

Multiple Alignment amp Tree View

31

PIR Hidden Markov ModelPIR Hidden Markov Modelhttppirgeorgetownedupirwwwsearchpirhmmhtml

HMM Model Building amp Sequence Search

One Protein Against All HMMs

All Proteins Against One HMM

33

Bibliography SubmissionBibliography Submission

View Bibliography Information

View Protein Entry

Submit Citation with Optional Categorization

S1

34

Bibliography Information Display (I)Bibliography Information Display (I)

From PIR-NREF

From Other Curated Database (eg SGD)

35

Bibliography Information Display (II)Bibliography Information Display (II)

From User Submission

From Computer-Mapping (eg Gene Symbol)

36

Oracle DemoOracle DemoJava Web Interface for Oracle Database Search (httppirgeorgetowneduiproclasshtml)

WebDB Interface to Oracle (WebDB) TablesViewsObjects FunctionsProceduresPackages

37

Proteomic BioinformaticsProteomic Bioinformatics

Large-Scale Analysis of Proteomic Data Homology Search for Pathways

• Database Demo
• PIR Web Site (httppirgeorgetownedu)
• Text Search Result with NULLNOT NULL
• Peptide Search Results
• PIR-NREF Search Result (I)
• PIR-NREF Search Result (II)
• PIR Pattern Search
• PIR Pattern Search Result (I)
• PIR Pattern Search Result (II)
• PIR Domain Display
• PIR-NREF Database (httppirgeorgetownedupirwwwsearchpirnrefshtml)
• PIR-NREF Report
• PIR-iProClass Database
• iProClass Sequence Report
• PDB Structure of Molecule Inosine-5-Monophosphate Dehydrogenase
• Related Sequences
• Protein Family Classification
• Protein FamilySuperfamily Definitions
• Protein Domain Definition
• Superfamily-Domain-Motif Relationship
• iProClass Superfamily List
• iProClass Superfamily Report
• Alignment and Tree View
• PIR-Protein Sequence Database
• PIR-PSD Entry
• BLASTFASTA Search
• PIR FASTA Search Result
• PIR Searches and Aligment
• PIR Hidden Markov Model
• Bibliography Submission
• Bibliography Information Display (I)
• Bibliography Information Display (II)
• Oracle Demo
• Proteomic Bioinformatics

31

PIR Hidden Markov ModelPIR Hidden Markov Modelhttppirgeorgetownedupirwwwsearchpirhmmhtml

HMM Model Building amp Sequence Search

One Protein Against All HMMs

All Proteins Against One HMM

33

Bibliography SubmissionBibliography Submission

View Bibliography Information

View Protein Entry

Submit Citation with Optional Categorization

S1

34

Bibliography Information Display (I)Bibliography Information Display (I)

From PIR-NREF

From Other Curated Database (eg SGD)

35

Bibliography Information Display (II)Bibliography Information Display (II)

From User Submission

From Computer-Mapping (eg Gene Symbol)

36

Oracle DemoOracle DemoJava Web Interface for Oracle Database Search (httppirgeorgetowneduiproclasshtml)

WebDB Interface to Oracle (WebDB) TablesViewsObjects FunctionsProceduresPackages

37

Proteomic BioinformaticsProteomic Bioinformatics

Large-Scale Analysis of Proteomic Data Homology Search for Pathways

• Database Demo
• PIR Web Site (httppirgeorgetownedu)
• Text Search Result with NULLNOT NULL
• Peptide Search Results
• PIR-NREF Search Result (I)
• PIR-NREF Search Result (II)
• PIR Pattern Search
• PIR Pattern Search Result (I)
• PIR Pattern Search Result (II)
• PIR Domain Display
• PIR-NREF Database (httppirgeorgetownedupirwwwsearchpirnrefshtml)
• PIR-NREF Report
• PIR-iProClass Database
• iProClass Sequence Report
• PDB Structure of Molecule Inosine-5-Monophosphate Dehydrogenase
• Related Sequences
• Protein Family Classification
• Protein FamilySuperfamily Definitions
• Protein Domain Definition
• Superfamily-Domain-Motif Relationship
• iProClass Superfamily List
• iProClass Superfamily Report
• Alignment and Tree View
• PIR-Protein Sequence Database
• PIR-PSD Entry
• BLASTFASTA Search
• PIR FASTA Search Result
• PIR Searches and Aligment
• PIR Hidden Markov Model
• Bibliography Submission
• Bibliography Information Display (I)
• Bibliography Information Display (II)
• Oracle Demo
• Proteomic Bioinformatics

33

Bibliography SubmissionBibliography Submission

View Bibliography Information

View Protein Entry

Submit Citation with Optional Categorization

S1

34

Bibliography Information Display (I)Bibliography Information Display (I)

From PIR-NREF

From Other Curated Database (eg SGD)

35

Bibliography Information Display (II)Bibliography Information Display (II)

From User Submission

From Computer-Mapping (eg Gene Symbol)

36

Oracle DemoOracle DemoJava Web Interface for Oracle Database Search (httppirgeorgetowneduiproclasshtml)

WebDB Interface to Oracle (WebDB) TablesViewsObjects FunctionsProceduresPackages

37

Proteomic BioinformaticsProteomic Bioinformatics

Large-Scale Analysis of Proteomic Data Homology Search for Pathways

• Database Demo
• PIR Web Site (httppirgeorgetownedu)
• Text Search Result with NULLNOT NULL
• Peptide Search Results
• PIR-NREF Search Result (I)
• PIR-NREF Search Result (II)
• PIR Pattern Search
• PIR Pattern Search Result (I)
• PIR Pattern Search Result (II)
• PIR Domain Display
• PIR-NREF Database (httppirgeorgetownedupirwwwsearchpirnrefshtml)
• PIR-NREF Report
• PIR-iProClass Database
• iProClass Sequence Report
• PDB Structure of Molecule Inosine-5-Monophosphate Dehydrogenase
• Related Sequences
• Protein Family Classification
• Protein FamilySuperfamily Definitions
• Protein Domain Definition
• Superfamily-Domain-Motif Relationship
• iProClass Superfamily List
• iProClass Superfamily Report
• Alignment and Tree View
• PIR-Protein Sequence Database
• PIR-PSD Entry
• BLASTFASTA Search
• PIR FASTA Search Result
• PIR Searches and Aligment
• PIR Hidden Markov Model
• Bibliography Submission
• Bibliography Information Display (I)
• Bibliography Information Display (II)
• Oracle Demo
• Proteomic Bioinformatics

34

Bibliography Information Display (I)Bibliography Information Display (I)

From PIR-NREF

From Other Curated Database (eg SGD)

35

Bibliography Information Display (II)Bibliography Information Display (II)

From User Submission

From Computer-Mapping (eg Gene Symbol)

36

Oracle DemoOracle DemoJava Web Interface for Oracle Database Search (httppirgeorgetowneduiproclasshtml)

WebDB Interface to Oracle (WebDB) TablesViewsObjects FunctionsProceduresPackages

37

Proteomic BioinformaticsProteomic Bioinformatics

Large-Scale Analysis of Proteomic Data Homology Search for Pathways

• Database Demo
• PIR Web Site (httppirgeorgetownedu)
• Text Search Result with NULLNOT NULL
• Peptide Search Results
• PIR-NREF Search Result (I)
• PIR-NREF Search Result (II)
• PIR Pattern Search
• PIR Pattern Search Result (I)
• PIR Pattern Search Result (II)
• PIR Domain Display
• PIR-NREF Database (httppirgeorgetownedupirwwwsearchpirnrefshtml)
• PIR-NREF Report
• PIR-iProClass Database
• iProClass Sequence Report
• PDB Structure of Molecule Inosine-5-Monophosphate Dehydrogenase
• Related Sequences
• Protein Family Classification
• Protein FamilySuperfamily Definitions
• Protein Domain Definition
• Superfamily-Domain-Motif Relationship
• iProClass Superfamily List
• iProClass Superfamily Report
• Alignment and Tree View
• PIR-Protein Sequence Database
• PIR-PSD Entry
• BLASTFASTA Search
• PIR FASTA Search Result
• PIR Searches and Aligment
• PIR Hidden Markov Model
• Bibliography Submission
• Bibliography Information Display (I)
• Bibliography Information Display (II)
• Oracle Demo
• Proteomic Bioinformatics

35

Bibliography Information Display (II)Bibliography Information Display (II)

From User Submission

From Computer-Mapping (eg Gene Symbol)

36

Oracle DemoOracle DemoJava Web Interface for Oracle Database Search (httppirgeorgetowneduiproclasshtml)

WebDB Interface to Oracle (WebDB) TablesViewsObjects FunctionsProceduresPackages

37

Proteomic BioinformaticsProteomic Bioinformatics

Large-Scale Analysis of Proteomic Data Homology Search for Pathways

• Database Demo
• PIR Web Site (httppirgeorgetownedu)
• Text Search Result with NULLNOT NULL
• Peptide Search Results
• PIR-NREF Search Result (I)
• PIR-NREF Search Result (II)
• PIR Pattern Search
• PIR Pattern Search Result (I)
• PIR Pattern Search Result (II)
• PIR Domain Display
• PIR-NREF Database (httppirgeorgetownedupirwwwsearchpirnrefshtml)
• PIR-NREF Report
• PIR-iProClass Database
• iProClass Sequence Report
• PDB Structure of Molecule Inosine-5-Monophosphate Dehydrogenase
• Related Sequences
• Protein Family Classification
• Protein FamilySuperfamily Definitions
• Protein Domain Definition
• Superfamily-Domain-Motif Relationship
• iProClass Superfamily List
• iProClass Superfamily Report
• Alignment and Tree View
• PIR-Protein Sequence Database
• PIR-PSD Entry
• BLASTFASTA Search
• PIR FASTA Search Result
• PIR Searches and Aligment
• PIR Hidden Markov Model
• Bibliography Submission
• Bibliography Information Display (I)
• Bibliography Information Display (II)
• Oracle Demo
• Proteomic Bioinformatics

36

Oracle DemoOracle DemoJava Web Interface for Oracle Database Search (httppirgeorgetowneduiproclasshtml)

WebDB Interface to Oracle (WebDB) TablesViewsObjects FunctionsProceduresPackages

37

Proteomic BioinformaticsProteomic Bioinformatics

Large-Scale Analysis of Proteomic Data Homology Search for Pathways

• Database Demo
• PIR Web Site (httppirgeorgetownedu)
• Text Search Result with NULLNOT NULL
• Peptide Search Results
• PIR-NREF Search Result (I)
• PIR-NREF Search Result (II)
• PIR Pattern Search
• PIR Pattern Search Result (I)
• PIR Pattern Search Result (II)
• PIR Domain Display
• PIR-NREF Database (httppirgeorgetownedupirwwwsearchpirnrefshtml)
• PIR-NREF Report
• PIR-iProClass Database
• iProClass Sequence Report
• PDB Structure of Molecule Inosine-5-Monophosphate Dehydrogenase
• Related Sequences
• Protein Family Classification
• Protein FamilySuperfamily Definitions
• Protein Domain Definition
• Superfamily-Domain-Motif Relationship
• iProClass Superfamily List
• iProClass Superfamily Report
• Alignment and Tree View
• PIR-Protein Sequence Database
• PIR-PSD Entry
• BLASTFASTA Search
• PIR FASTA Search Result
• PIR Searches and Aligment
• PIR Hidden Markov Model
• Bibliography Submission
• Bibliography Information Display (I)
• Bibliography Information Display (II)
• Oracle Demo
• Proteomic Bioinformatics

37

Proteomic BioinformaticsProteomic Bioinformatics

Large-Scale Analysis of Proteomic Data Homology Search for Pathways

• Database Demo
• PIR Web Site (httppirgeorgetownedu)
• Text Search Result with NULLNOT NULL
• Peptide Search Results
• PIR-NREF Search Result (I)
• PIR-NREF Search Result (II)
• PIR Pattern Search
• PIR Pattern Search Result (I)
• PIR Pattern Search Result (II)
• PIR Domain Display
• PIR-NREF Database (httppirgeorgetownedupirwwwsearchpirnrefshtml)
• PIR-NREF Report
• PIR-iProClass Database
• iProClass Sequence Report
• PDB Structure of Molecule Inosine-5-Monophosphate Dehydrogenase
• Related Sequences
• Protein Family Classification
• Protein FamilySuperfamily Definitions
• Protein Domain Definition
• Superfamily-Domain-Motif Relationship
• iProClass Superfamily List
• iProClass Superfamily Report
• Alignment and Tree View
• PIR-Protein Sequence Database
• PIR-PSD Entry
• BLASTFASTA Search
• PIR FASTA Search Result
• PIR Searches and Aligment
• PIR Hidden Markov Model
• Bibliography Submission
• Bibliography Information Display (I)
• Bibliography Information Display (II)
• Oracle Demo
• Proteomic Bioinformatics