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PPIP: Automated Software for Identification of Bioactive Endogenous Peptides
Mingqiang Rong1, Baojin Zhou2, Ruo Zhou2
1The National & Local Joint Engineering Laboratory of Animal Peptide Drug Development, College of Life Sciences , Hunan Normal University , Changsha 410081 , Hunan , China.
Abstract:
Endogenous peptides play an important role in multiple biological processes in many species. Liquid chromatography coupled to tandem mass spectrometry (LC-MS/MS) is an important technique for detecting these peptides on a large scale. We present PPIP, which is a dedicated peptidogenomics software for identifying endogenous peptides based on peptidomics and RNA-Seq data. This software automates the de novo transcript assembly based on RNA-Seq data, construction of a protein reference database based on the de novo assembled transcripts, peptide identification, function analysis, and HTML-based report generation. Different function components are integrated using Docker technology. The Docker image of PPIP is available at https://hub.docker.com/r/shawndp/ppip , and the source code under GPL-3 license is available at https://github.com/Shawn-Xu/PPIP . A user manual of PPIP is available at https://shawn-xu.github.io/PPIP .
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