PPIP: An automated software for identification of bioactive endogenous peptides.
JOURNAL OF PROTEOME RESEARCH(2019)
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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Key words
bioinformatics,proteogenomics,proteomics,peptidomics,peptidogenomics
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