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

Tovchigrechko, A.; Venepally, P.; Payne, S. H.

doi:10.1093/bioinformatics/btu051

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

Journal Article · Mon Jan 27 00:00:00 EST 2014 · Bioinformatics

DOI:https://doi.org/10.1093/bioinformatics/btu051· OSTI ID:1625286

Tovchigrechko, A. ^[1]; Venepally, P. ^[2]; Payne, S. H. ^[3]

J. Craig Venter Inst., Inc., Rockville, MD (United States); DOE/OSTI
J. Craig Venter Inst., Inc., Rockville, MD (United States)
Pacific Northwest National Lab. (PNNL), Richland, WA (United States)

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.

Research Organization:: Pacific Northwest National Laboratory (PNNL), Richland, WA (United States)

Sponsoring Organization:: USDOE Office of Science (SC), Biological and Environmental Research (BER). Biological Systems Science Division

Grant/Contract Number:: AC05-76RL01830

OSTI ID:: 1625286

Journal Information:: Bioinformatics, Journal Name: Bioinformatics Journal Issue: 10 Vol. 30; ISSN 1367-4803

Publisher:: International Society for Computational Biology - Oxford University PressCopyright Statement

Country of Publication:: United States

Language:: English

References (9)

The integrated microbial genomes (IMG) system in 2007: data content and analysis tool extensions Markowitz, V. M.; Szeto, E.; Palaniappan, K. Nucleic Acids Research, Vol. 36, Issue Database https://doi.org/10.1093/nar/gkm846	journal	December 2007
The Taverna workflow suite: designing and executing workflows of Web Services on the desktop, web or in the cloud Wolstencroft, Katherine; Haines, Robert; Fellows, Donal Nucleic Acids Research, Vol. 41, Issue W1 https://doi.org/10.1093/nar/gkt328	journal	May 2013
Galaxy: A platform for interactive large-scale genome analysis Giardine, B. Genome Research, Vol. 15, Issue 10 https://doi.org/10.1101/gr.4086505	journal	September 2005
The Proteogenomic Mapping Tool Sanders, William S.; Wang, Nan; Bridges, Susan M. BMC Bioinformatics, Vol. 12, Issue 1 https://doi.org/10.1186/1471-2105-12-115	journal	January 2011
The RAST Server: Rapid Annotations using Subsystems Technology Aziz, Ramy K.; Bartels, Daniela; Best, Aaron A. BMC Genomics, Vol. 9, Issue 1, Article No. 75 https://doi.org/10.1186/1471-2164-9-75	journal	January 2008
Proteogenomic Analysis of Bacteria and Archaea: A 46 Organism Case Study Venter, Eli; Smith, Richard D.; Payne, Samuel H. PLoS ONE, Vol. 6, Issue 11 https://doi.org/10.1371/journal.pone.0027587	journal	November 2011
Plant Proteogenomics: From Protein Extraction to Improved Gene Predictions Chapman, Brett; Castellana, Natalie; Apffel, Alex Methods in Molecular Biology https://doi.org/10.1007/978-1-62703-360-2_21	book	January 2013
Peppy: Proteogenomic Search Software Risk, Brian A.; Spitzer, Wendy J.; Giddings, Morgan C. Journal of Proteome Research, Vol. 12, Issue 6 https://doi.org/10.1021/pr400208w	journal	May 2013
Proteogenomic Analysis of Bradyrhizobium japonicum USDA110 Using Genosuite, an Automated Multi-algorithmic Pipeline Kumar, Dhirendra; Yadav, Amit Kumar; Kadimi, Puneet Kumar Molecular & Cellular Proteomics, Vol. 12, Issue 11 https://doi.org/10.1074/mcp.M112.027169	journal	November 2013

Cited By (6)

Proteomics progresses in microbial physiology and clinical antimicrobial therapy Chen, B.; Zhang, D.; Wang, X. European Journal of Clinical Microbiology & Infectious Diseases, Vol. 36, Issue 3 https://doi.org/10.1007/s10096-016-2816-4	journal	November 2016
An integrative strategy to identify the entire protein coding potential of prokaryotic genomes by proteogenomics Omasits, Ulrich; Varadarajan, Adithi R.; Schmid, Michael Genome Research, Vol. 27, Issue 12 https://doi.org/10.1101/gr.218255.116	journal	November 2017
The bacterial proteogenomic pipeline Uszkoreit, Julian; Plohnke, Nicole; Rexroth, Sascha BMC Genomics, Vol. 15, Issue S9 https://doi.org/10.1186/1471-2164-15-s9-s19	journal	December 2014
A Pilot Proteogenomic Study with Data Integration Identifies MCT1 and GLUT1 as Prognostic Markers in Lung Adenocarcinoma Stewart, Paul A.; Parapatics, Katja; Welsh, Eric A. PLOS ONE, Vol. 10, Issue 11 https://doi.org/10.1371/journal.pone.0142162	journal	November 2015
Proteogenomics from a bioinformatics angle: A growing field: PROTEOGENOMICS FROM A BIOINFORMATICS ANGLE Menschaert, Gerben; Fenyö, David Mass Spectrometry Reviews, Vol. 36, Issue 5 https://doi.org/10.1002/mas.21483	journal	December 2015
Proteogenomics: concepts, applications and computational strategies Nesvizhskii, Alexey I. Nature Methods, Vol. 11, Issue 11 https://doi.org/10.1038/nmeth.3144	journal	October 2014

Similar Records

Proteogenomic analysis of bacteria and archaea: A 46 organism case study

Journal Article · Wed Nov 16 23:00:00 EST 2011 · PLoS One · OSTI ID:1033067

PRAP: An automated de novo repeat finder pipeline for prokaryotic genomes

Conference · Sun Dec 31 23:00:00 EST 2006 · OSTI ID:985744

GenePRIMP: A Gene Prediction Improvement Pipeline For Prokaryotic Genomes

Software · Thu Jul 08 00:00:00 EDT 2010 · OSTI ID:1431050

Related Subjects

59 BASIC BIOLOGICAL SCIENCES
97 MATHEMATICS AND COMPUTING
Biochemistry & Molecular Biology
Biotechnology & Applied Microbiology
Computer Science
Mathematical & Computational Biology
Mathematics

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

Citation Formats

References (9)

Cited By (6)

Similar Records

Related Subjects