PPIP: Automated Software for Identification of Bioactive Endogenous Peptides

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.