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

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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

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Acknowledgements

The authors thank Professor Gu Xiaochen of Peking University, China for helpful discussions.

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Authors and Affiliations

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

    Ying Jiang, Eric L. Gustafson, Maureen Laverty, Jonathan R. Greene, Marvin L. Bayne, Joseph A. Hedrick & Nicholas J. Murgolo

  2. Centre of Bioinformatics, College of Life Sciences, Peking University, Beijing 100871, P.R. China

    Ying Jiang, Ge Gao, Gang Fang, Yanbin Yin, Yong Zhang & Jingchu Luo

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  1. Ying Jiang
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Correspondence to Ying Jiang.

MEDLINE Abstract

MEDLINE Abstract

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http://hmmer.wustl.edu

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http://www.infobiogen.fr/~gracy/domo/home.htm

http://blocks.fhcrc.org

http://motif.stanford.edu/emotif/

http://www.ebi.ac.uk/fasta3/

http://bighost.area.ba.cnr.it/BIG/Patsearch/Patsearch.html

http://blocks.fhcrc.org/blocks/impala.html

http://www.ncbi.nlm.nih.gov/Structure/cdd/wrpsb.cgi

http://www.ncbi.nlm.nih.gov/BLAST/

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Jiang, Y., Gao, G., Fang, G. et al. PepPat, a pattern-based oligopeptide homology search method and the identification of a novel tachykinin-like peptide . Mamm Genome 14, 341–349 (2003). https://doi.org/10.1007/s00335-002-3061-y

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  • DOI: https://doi.org/10.1007/s00335-002-3061-y

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