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

Summary: 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...

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Detalles Bibliográficos
Autores principales: Tovchigrechko, Andrey, Venepally, Pratap, Payne, Samuel H.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Oxford University Press 2014
Materias:
Applications Notes
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4016709/
https://www.ncbi.nlm.nih.gov/pubmed/24470574
http://dx.doi.org/10.1093/bioinformatics/btu051
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author Tovchigrechko, Andrey
Venepally, Pratap
Payne, Samuel H.
author_facet Tovchigrechko, Andrey
Venepally, Pratap
Payne, Samuel H.
author_sort Tovchigrechko, Andrey
collection PubMed
description Summary: 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. Availability and implementation: 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. Contact: atovtchi@jcvi.org
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spelling pubmed-40167092014-05-12 PGP: parallel prokaryotic proteogenomics pipeline for MPI clusters, high-throughput batch clusters and multicore workstations Tovchigrechko, Andrey Venepally, Pratap Payne, Samuel H. Bioinformatics Applications Notes Summary: 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. Availability and implementation: 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. Contact: atovtchi@jcvi.org Oxford University Press 2014-05-15 2014-01-27 /pmc/articles/PMC4016709/ /pubmed/24470574 http://dx.doi.org/10.1093/bioinformatics/btu051 Text en © The Author 2014. Published by Oxford University Press. http://creativecommons.org/licenses/by/3.0/ This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/3.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Applications Notes
Tovchigrechko, Andrey
Venepally, Pratap
Payne, Samuel H.
PGP: parallel prokaryotic proteogenomics pipeline for MPI clusters, high-throughput batch clusters and multicore workstations
title PGP: parallel prokaryotic proteogenomics pipeline for MPI clusters, high-throughput batch clusters and multicore workstations
title_full PGP: parallel prokaryotic proteogenomics pipeline for MPI clusters, high-throughput batch clusters and multicore workstations
title_fullStr PGP: parallel prokaryotic proteogenomics pipeline for MPI clusters, high-throughput batch clusters and multicore workstations
title_full_unstemmed PGP: parallel prokaryotic proteogenomics pipeline for MPI clusters, high-throughput batch clusters and multicore workstations
title_short PGP: parallel prokaryotic proteogenomics pipeline for MPI clusters, high-throughput batch clusters and multicore workstations
title_sort pgp: parallel prokaryotic proteogenomics pipeline for mpi clusters, high-throughput batch clusters and multicore workstations
topic Applications Notes
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4016709/
https://www.ncbi.nlm.nih.gov/pubmed/24470574
http://dx.doi.org/10.1093/bioinformatics/btu051
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