EBI is an Outstation of the European Molecular Biology Laboratory. EBI patent related services...

EBI is an Outstation of the European Molecular Biology Laboratory.

EBI patent related services

Jennifer McDowallSenior Scientist, EMBL-EBI

3rd Annual Forum for SMEs

September 3-4th 2009

Overview

Databases available

Sequence archives

Searching the database


Databases available…


September 2009nucl > 9.4m sequencesprot > 2.5m sequences

GenBankGenBank

EMBLEMBL

DDBJDDBJ

EPOEPO

USPTOUSPTO JPOJPO

EPO policy: data released topublic (and to EMBL) 18 months after the patent application date, independent of whether patent has been granted.

.

Sequence data from patent literature


EMBLEMBL

Know the Data…Nucleotides


Release and updates

EMBLEMBL


Divided into classes and divisions...

Release and updates

ANN – Annotated Constructed Seq PAT – Patent

CON – Constructed Sequence STS – Sequence Tagged Site

EST – Expressed Sequence Tag STD – Standard

GSS – Genome Survey Sequence TPA – Third Party Annotation

HTC – High Throughput cDNA TSA – Transcriptome Shotgun Assembly

HTG – High Throughput Genome WGS – Whole Genome Shotgun


EMBLEMBL



Release and updates


HUM – Human

MUS – Mouse

ROD – Rodent (excluding mouse)

MAM – Mammal (excluding human, mouse, rodent)

VRT – Vertebrate (excluding human, mouse, rodent, mammal)

FUN – Fungi PRO – Prokaryote ENV – Environment

INV – Invertebrate PHG – Phage SYN – Synthetic

PLN – Plant VIR – Viral TGN – Transgenic

UNC – Unclassified

EMBLEMBL



Release and updates

Supplementary sets: EMBL-CDS, EMBL-MGA


Specialist databases: • Immunoglobulins (IMGT/HLA, IMGT/LIGM)

• Alternative splicing (ASDT)

• Completed proteomes (Ensembl, Integr8)

• Variation (HGVBase, dbSNP)


EMBL Patent Sequence Entry

Version, dates, archive

Patent number, title, link to patent


UniProtUniProt

Know the Data…Proteins

Release and updates

UniProtUniProt


Divided into 3 sections:

Release and updates

UniProtKBUniProtKB

• Taxonomic info • Annotated sequence

UniRefUniRef

• Combines sequences by % ID

• UniRef100, 90, 50

UniParcUniParc

• Protein archive• Covers ALL proteins (including UniMess)


SwissProt TrEMBL

Manual annotation

Automatic annotation

UniProtUniProt


Divided into 3 sections

Release and updates

Specialist databases linked to UniProt: • Structure (PDBe, SGT)

• Immunoglobulins (IMGT/HLA)

• Alternative splicing (ASDT)

• Completed proteomes (Ensembl, Integr8)

• Protein interactions (IntAct)

• Protein signatures (InterPro)

• Patent proteins (EPO, USTPO, JPO, KIPO)



Bulk download

http://www.ebi.ac.uk/patentdata/

Nucleotide sequences

Protein sequences


Bulk download

ftp.ebi.ac.uk/pub/databases/embl/patent/

Sequence archives…


• EMBL nucleotide sequence version archive (SVA)www.ebi.ac.uk/embl/sva

• UniSave – UniProt sequence/annotation version archivewww.ebi.ac.uk/uniprot/unisave

Sequence archives


EMBL sequence version archive (SVA)


View old entries

Enter accession

#


Sequence record from EMBL SVA


Comparing versions in EMBL SVA

Select and compare versions


UniProtKB sequence annotation version server - UniSave

Enter accession

#


UniSave results

Select and compare versions

View old entries


Searching the databases…

EB-eye search by patent number

Search for patent WO0146262


EB-eye search by patent number



EB-eye nucleotide sequences from WO0146262

Sequence Similarity Search Tools


Toolbox

BLASTBLAST

NCBI-BLASTNCBI-BLAST

Wu-BLASTWu-BLAST

FASTAFASTA

FASTA suiteFASTA suite

Smith-WatermanSmith-Waterman

MPsrchMPsrch

ScanPSScanPS

SSEARCHSSEARCH

PSI searchPSI search

PSI-SEARCHPSI-SEARCH

PSI-BLASTPSI-BLAST

Blast v. patent nucleotide sequences


Fasta v. patent protein sequences

Tools: Genomes & Proteomes FASTA


Database size

Que

ry le

ngth

FASTA

WU-BLAST

NCBI BLAST

PSI-SEARCH

When to use which search?


PDB Swiss-Prot UniRef50 UniRef 90 UniRef100 UniProtKB UniParc

FASTA

WU-BLAST

NCBI BLAST

PSI-SEARCH

time

to s

earc

hWhen to use which search?


InterProScan protein signature search


www.ebi.ac.uk/interpro/

InterPro signature database



Some search guidelines…

Search Guidelines

#1 Use the most appropriate tool for your search

- Don’t assume one tool will cater to all your search needs

Database size

Que

ry le

ngth

FASTA

WU-BLAST

NCBI BLAST

PSI-SEARCH


Search Guidelines


#2 Best search option protein seq v. protein DB

2nd translated DNA seq v. protein DB

3rd DNA seq v. DNA DB

Worst protein seq v. transl DNA BD


Search Guidelines



#3 Search the smallest DB likely to have your sequence

#4 Check statistics – histograms...

#5 Change parameters when necessary (gap penalties, scoring matrices...)

#6 Don’t assume homologues have the same function

• Orthologs have similar functions

• Paralogs acquire different functions


Search Guidelines



#3 Search the smallest DB likely to have your sequence

#4 Check statistics – histograms...

#5 Change parameters when necessary (gap penalties, scoring matrices...)

#6 Don’t assume homologues have the same function


#7 Use multiple sequence alignments to validate relatedness

#8 Consider filtering low complexity regions

Typical workflow

searchreview Check stats

compareevolutionfunction


EBI is an Outstation of the European Molecular Biology Laboratory.

Contacts:http://www.ebi.ac.uk/support/

EBI is an Outstation of the European Molecular Biology Laboratory. EBI patent related services...

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