Open AccessPGP: parallel prokaryotic proteogenomics pipeline for MPI clusters, high-throughput batch clusters and multicore workstations
Author(s) -
Andrey Tovchigrechko,
Pratap Venepally,
Samuel Payne
Publication year - 2014
Publication title -
bioinformatics
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 3.599
H-Index - 390
eISSN - 1367-4811
pISSN - 1367-4803
DOI - 10.1093/bioinformatics/btu051
Subject(s) - computer science , proteogenomics , software portability , pipeline (software) , python (programming language) , workstation , mit license , multi core processor , annotation , operating system , software , parallel computing , genome , biology , genomics , artificial intelligence , biochemistry , gene
We present the first public release of our proteogenomic annotation pipeline. We have previously used our original unreleased implementation to improve the annotation of 46 diverse prokaryotic genomes by discovering novel genes, post-translational modifications and correcting the erroneous annotations by analyzing proteomic mass-spectrometry data. This public version has been redesigned to run in a wide range of parallel Linux computing environments and provided with the automated configuration, build and testing facilities for easy deployment and portability.
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