PepPat，一种基于模式的寡肽同源性搜索方法及一种新型速激肽样肽的鉴定。

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

作者信息

Jiang Ying, Gao Ge, Fang Gang, Gustafson Eric L, Laverty Maureen, Yin Yanbin, Zhang Yong, Luo Jingchu, Greene Jonathan R, Bayne Marvin L, Hedrick Joseph A, Murgolo Nicholas J

机构信息

Bioinformatics/Genomics Research, Schering-Plough Research Institute, 2015 Gallopjng Hill Road, Kenilworth, NJ 07033, USA.

出版信息

Mamm Genome. 2003 May;14(5):341-9. doi: 10.1007/s00335-002-3061-y.

DOI:10.1007/s00335-002-3061-y

PMID:12856286

Abstract

UNLABELLED

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.

摘要

未标注

描述了一种将模式匹配与相似性评分相结合的混合方法PepPat。我们还报告了PepPat在鉴定一种新型速激肽样肽中的应用。PepPat将查询肽和肽内用户指定的正则表达式模式作为输入。它首先执行数据库模式匹配，然后根据候选序列与查询肽的相似性对其进行排名。PepPat在跨越区域的模式上计算相似性，提高了PepPat对短查询肽的敏感性。PepPat还可以在目标序列中搜索用户指定数量的重复模式出现情况。我们展示了PepPat在短肽配体挖掘中的应用。作为一个验证示例，我们报告了一种新型速激肽样肽C14TKL-1的鉴定，并表明它是一种NK1（神经激肽受体1）激动剂，其信息在人类外周广泛表达。