PepPat, a pattern-based oligopeptide homology search method and the identification of a novel tachykinin-like peptide.
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.
Jiang
Ying
Y
Bioinformatics/Genomics Research, Schering-Plough Research Institute, 2015 Gallopjng Hill Road, Kenilworth, NJ 07033, USA. ying.Jiang@spcorp.com
Gao
Ge
G
Fang
Gang
G
Gustafson
Eric L
EL
Laverty
Maureen
M
Yin
Yanbin
Y
Zhang
Yong
Y
Luo
Jingchu
J
Greene
Jonathan R
JR
Bayne
Marvin L
ML
Hedrick
Joseph A
JA
Murgolo
Nicholas J
NJ
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
D017931:DNA Primers; D009842:Oligopeptides; D018040:Receptors, Neurokinin-1; D015320:Tachykinins