PROTEIN PATTERN DATABASES. PROTEIN SEQUENCES SUPERFAMILY FAMILY DOMAIN MOTIF SITE RESIDUE.
Protein Databases
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Protein Databases
EBI – European Bioinformatics Institute
http://www.ebi.ac.uk/
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What is the difference between
dealing with nucleotide DBs and
protein DBs?
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Protein information
Name & description.
Gene encoded from.
Organism.
Function.
Enzyme? Ligands?
PTMs? Interactions?
Biological processes.
Structure.
Sequence.
More...
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Protein DBs Swiss-Prot - manually annotated.
TrEMBL – translated EMBL, automatically
annotated.
RefSeq – Reference Sequence for proteins,
currated.
UniRef – The UniProt Reference Clusters.
PIR - Protein Information Resource.
PDB – Protein Data Bank – structure.
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Databases growth
www.genome.jp/en/db_growth.html
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Protein NamesDifferent DBs – different accessions
DBAccessions
TrEMBLP12345
Swiss-ProtMAPK_HUMAN
RefSeqNP_123456
XP_123456
UniRefUniRef100_P99999
UniRef90_P99999
UniRef50_P99999
EnsemblENSP00000123456
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EBI interface
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EB-eye search
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EB-eye search
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NCBI - Entrez
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UniProt Knowledgebase a complete annotated protein sequence database
UniProtThe Universal Protein Resource for protein sequences .
UniProt ArchiveA non-redundant archive of protein sequences extracted from public databases and contains only protein sequences.
UniProt/UniRefFeatures clustering of similar sequences to yield a representative subset of sequences. This produces very fast search times.
UniProt/UniMESA repository specifically developed for metagenomic and environmental data.
UniProtKB/Swiss-Prot
An annotated protein sequence database. Part of the UniProtKB.
UniProtKB/TrEMBLA computer generated protein database enriched with automated classification and annotation. Part of the UniProtKB.
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http://beta.uniprot.org/
What’s in UniProt?
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How is it built?
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PIR – Protein Information Resource
Protein Family Classification System
Integrated
Protein
Knowledgebase
Integrated Protein Literature, Information and Knowledge