PPIP: Automated Software for Identification of Bioactive Endogenous Peptides
2018
Rong, Mingqiang | Zhou, Baojin | Zhou, Ruo | Liao, Qiong | Zeng, Yong | Xu, Shaohang | Liu, Zhonghua
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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