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CoPS: Comprehensive Peptide Signature database.

Tulika Prakash1, Mamta Khandelwal, Dipayan Dasgupta

  • 1G.N.R. Knowledge Center for Genome Informatics, Institute of Genomics and Integrative Biology, (Formerly Centre for Biochemical Technology), CSIR, Delhi University Campus, Mall Road, Delhi 110 007, India.

Bioinformatics (Oxford, England)
|May 29, 2004
PubMed
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A new database, Comprehensive database of invariant Peptide Signatures (CoPS), identifies critical functional residues in proteins. This resource aids in assigning functions to unknown proteins across bacterial and human genomes.

Area of Science:

  • Bioinformatics
  • Proteomics
  • Genomics

Background:

  • Invariant Peptide Signatures (CoPS) are conserved amino acid sequences found across multiple organisms.
  • Identifying these signatures aids in understanding protein function and evolution.
  • Existing databases lack comprehensive collections of cross-species conserved peptide signatures.

Purpose of the Study:

  • To develop a comprehensive database of invariant Peptide Signatures (CoPS).
  • To provide functional, structural, and pathway information for proteins containing these signatures.
  • To enable functional assignment for unknown proteins.

Main Methods:

  • Compiled 12,076 invariant Peptide Signatures from 52 bacterial genomes.
  • Ensured minimum occurrence in seven bacterial species for signature inclusion.

Related Experiment Videos

  • Integrated data on protein function, structure, biochemical pathways, and cross-database matches (PROSITE, Pfam).

    • Main Results:

    • The CoPS database contains 12,076 signatures from 52 bacterial genomes, present in ~1250 functional proteins.
    • Database includes cross-references to other motif databases and human proteome data.
    • Successfully assigned functions to 2605 hypothetical bacterial proteins and 112 unknown human proteins.

    Conclusions:

    • The CoPS database is a valuable resource for identifying critical functional residues and protein structural determinants.
    • Facilitates functional annotation of uncharacterized proteins in various genomes.
    • Demonstrates broad applicability in comparative genomics and proteomics research.