title: PepPat, a pattern-based oligopeptide homology search method and the identification of a novel tachykinin-like peptide.
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.
  
  
  BACKGROUND
  PepPat is offered online at: http://peppat.cbi.pku.edu.cn.
authors.affiliation: Bioinformatics/Genomics Research, Schering-Plough Research Institute, 2015 Gallopjng Hill Road, Kenilworth, NJ 07033, USA. ying.Jiang@spcorp.com
authors.forename: Ying
authors.initials: Y
authors.lastname: Jiang
authors.forename: Ge
authors.initials: G
authors.lastname: Gao
authors.forename: Gang
authors.initials: G
authors.lastname: Fang
authors.forename: Eric L
authors.initials: EL
authors.lastname: Gustafson
authors.forename: Maureen
authors.initials: M
authors.lastname: Laverty
authors.forename: Yanbin
authors.initials: Y
authors.lastname: Yin
authors.forename: Yong
authors.initials: Y
authors.lastname: Zhang
authors.forename: Jingchu
authors.initials: J
authors.lastname: Luo
authors.forename: Jonathan R
authors.initials: JR
authors.lastname: Greene
authors.forename: Marvin L
authors.initials: ML
authors.lastname: Bayne
authors.forename: Joseph A
authors.initials: JA
authors.lastname: Hedrick
authors.forename: Nicholas J
authors.initials: NJ
authors.lastname: Murgolo
mesh_terms: D000465:Algorithms; D017931:DNA Primers / Q000737:chemistry; D016208:Databases, Factual; D005821:Genetic Techniques; D006801:Humans; D009842:Oligopeptides / Q000235:genetics* / Q000378:metabolism; D016133:Polymerase Chain Reaction; D018040:Receptors, Neurokinin-1 / Q000235:genetics* / Q000378:metabolism; D016415:Sequence Alignment; D017386:Sequence Homology, Amino Acid; D015320:Tachykinins / Q000235:genetics* / Q000378:metabolism
chemical_list: D017931:DNA Primers; D009842:Oligopeptides; D018040:Receptors, Neurokinin-1; D015320:Tachykinins