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Bioinformatics Advance Access published online on May 27, 2004
Bioinformatics, doi:10.1093/bioinformatics/bth325
Bioinformatics © Oxford University Press 2004; all rights reserved
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Received October 22, 2003
Revised April 16, 2004
Accepted April 28, 2004

Article

CoPS: comprehensive peptide signature database

Tulika Prakash 1, Mamta Khandelwal 1, Dipayan Dasgupta 1, Debasis Dash 1*, Samir K. Brahmachari 1

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

* To whom correspondence should be addressed. E-mail: ddash{at}igib.res.in.


  Abstract

Summary: We present the development of a Comprehensive database of 12,076 invariant Peptide Signatures (CoPS) derived from 52 bacterial genomes with a minimum occurrence in at least seven organisms. These peptides were observed in functionally similar proteins and are distributed over nearly 1,250 different functional proteins. The database provides function, structure and occurrence in biochemical pathways of the proteins containing these signature peptides. It houses additional information on the signature peptides such as identical match in other motifs/patterns (e.g. PROSITE, BLOCKS, PRINTS, Pfam) databases and the database of interacting proteins (DIP), human proteome and mutation effects on these signature peptides. There is a wide applicability of this database in identification of critical functional residues in proteins. The database also facilitates the identification of folding nucleus/structural determinants in proteins and functional assignment to yet unknown proteins. We demonstrate functional assignment to 2,605 hypothetical proteins in bacterial genomes and 112 unknown proteins in human using this database.

Availability: The database can be freely accessed through the following URL: http://203.195.151.46/copsv2/index.html or http://203.90.127.70/copsv2/index.html.

Supplementary Information: http://203.195.151.46/copsv2/aboutcops.html; http://203.90.127.70/copsv2/aboutcops.html.


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