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Mamm Genome. 2003 May;14(5):341-9.

PepPat, a pattern-based oligopeptide homology search method and the identification of a novel tachykinin-like peptide.

Author information

1
Bioinformatics/Genomics Research, Schering-Plough Research Institute, 2015 Gallopjng Hill Road, Kenilworth, NJ 07033, USA. ying.Jiang@spcorp.com

Erratum in

  • Mamm Genome. 2003 Aug;14(8):580.

Abstract

PepPat, a hybrid method that combines pattern matching with similarity scoring, is described. We also report PepPat's application in the identification of a novel tachykinin-like peptide. PepPat takes as input a query peptide and a user-specified regular expression pattern within the peptide. It first performs a database pattern match and then ranks candidates on the basis of their similarity to the query peptide. PepPat calculates similarity over the pattern spanning region, enhancing PepPat's sensitivity for short query peptides. PepPat can also search for a user-specified number of occurrences of a repeated pattern within the target sequence. We illustrate PepPat's application in short peptide ligand mining. As a validation example, we report the identification of a novel tachykinin-like peptide, C14TKL-1, and show it is an NK1 (neuokinin receptor 1) agonist whose message is widely expressed in human periphery.

AVAILABILITY:

PepPat is offered online at: http://peppat.cbi.pku.edu.cn.

PMID:
12856286
DOI:
10.1007/s00335-002-3061-y
[Indexed for MEDLINE]

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