PGP: parallel prokaryotic proteogenomics pipeline for MPI clusters, high-throughput batch clusters and multicore workstations.
CONCLUSIONS
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.


METHODS
Source code is freely available from https://bitbucket.org/andreyto/proteogenomics under GPL license. It is implemented in Python and C++. It bundles the Makeflow engine to execute the workflows.


BACKGROUND
atovtchi@jcvi.org.
J. Craig Venter Institute, 9704 Medical Center Drive, Rockville, MD 20850 and Pacific Northwest National Laboratory, 902 Battelle Blvd., Richland, WA 99354, USA.
Andrey
A
Tovchigrechko
Pratap
P
Venepally
Samuel H
SH
Payne
D016000:Cluster Analysis; D023281:Genomics / Q000379:methods*; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods*; D013058:Mass Spectrometry; D011387:Prokaryotic Cells / Q000737:chemistry*; D040901:Proteomics / Q000379:methods*; D012984:Software