The standard operating procedure of the DOE-JGI Microbial Genome Annotation Pipeline (MGAP v.4)

Huntemann, Marcel; Ivanova, Natalia N.; Mavromatis, Konstantinos; Tripp, H. James; Paez-Espino, David; Palaniappan, Krishnaveni; Szeto, Ernest; Pillay, Manoj; Chen, I-Min A.; Pati, Amrita; Nielsen, Torben; Markowitz, Victor M.; Kyrpides, Nikos C.

doi:10.1186/s40793-015-0077-y

The standard operating procedure of the DOE-JGI Microbial Genome Annotation Pipeline (MGAP v.4)

Journal Article · Mon Oct 26 00:00:00 EDT 2015 · Standards in Genomic Sciences

DOI:https://doi.org/10.1186/s40793-015-0077-y· OSTI ID:1618953

Huntemann, Marcel; Ivanova, Natalia N.; Mavromatis, Konstantinos; Tripp, H. James; Paez-Espino, David; Palaniappan, Krishnaveni; Szeto, Ernest; Pillay, Manoj; Chen, I-Min A.; Pati, Amrita; Nielsen, Torben; Markowitz, Victor M.; Kyrpides, Nikos C.

Abstract

The DOE-JGI Microbial Genome Annotation Pipeline performs structural and functional annotation of microbial genomes that are further included into the Integrated Microbial Genome comparative analysis system. MGAP is applied to assembled nucleotide sequence datasets that are provided via the IMG submission site. Dataset submission for annotation first requires project and associated metadata description in GOLD. The MGAP sequence data processing consists of feature prediction including identification of protein-coding genes, non-coding RNAs and regulatory RNA features, as well as CRISPR elements. Structural annotation is followed by assignment of protein product names and functions.

View Journal Article

Sponsoring Organization:: USDOE

Grant/Contract Number:: AC02-05CH11231

OSTI ID:: 1618953

Alternate ID(s):: OSTI ID: 1256940
OSTI ID: 1378607

Journal Information:: Standards in Genomic Sciences, Journal Name: Standards in Genomic Sciences Journal Issue: 1 Vol. 10; ISSN 1944-3277

Publisher:: Springer Science + Business MediaCopyright Statement

Country of Publication:: United Kingdom

Language:: English

References (20)

Predicting transmembrane protein topology with a hidden markov model: application to complete genomes11Edited by F. Cohen Krogh, Anders; Larsson, Björn; von Heijne, Gunnar Journal of Molecular Biology, Vol. 305, Issue 3 https://doi.org/10.1006/jmbi.2000.4315	journal	January 2001
A Fast and Symmetric DUST Implementation to Mask Low-Complexity DNA Sequences Morgulis, Aleksandr; Gertz, E. Michael; Schäffer, Alejandro A. Journal of Computational Biology, Vol. 13, Issue 5 https://doi.org/10.1089/cmb.2006.13.1028	journal	June 2006
Infernal 1.0: inference of RNA alignments Nawrocki, E. P.; Kolbe, D. L.; Eddy, S. R. Bioinformatics, Vol. 25, Issue 10 https://doi.org/10.1093/bioinformatics/btp157	journal	March 2009
Search and clustering orders of magnitude faster than BLAST Edgar, Robert C. Bioinformatics, Vol. 26, Issue 19, p. 2460-2461 https://doi.org/10.1093/bioinformatics/btq461	journal	August 2010
InterProScan 5: genome-scale protein function classification Jones, P.; Binns, D.; Chang, H. -Y. Bioinformatics, Vol. 30, Issue 9 https://doi.org/10.1093/bioinformatics/btu031	journal	January 2014
tRNAscan-SE: A Program for Improved Detection of Transfer RNA Genes in Genomic Sequence Lowe, Todd M.; Eddy, Sean R. Nucleic Acids Research, Vol. 25, Issue 5 https://doi.org/10.1093/nar/25.5.0955	journal	March 1997
Rfam: annotating non-coding RNAs in complete genomes Griffiths-Jones, S. Nucleic Acids Research, Vol. 33, Issue Database issue https://doi.org/10.1093/nar/gki081	journal	December 2004
TIGRFAMs and Genome Properties: tools for the assignment of molecular function and biological process in prokaryotic genomes Selengut, J. D.; Haft, D. H.; Davidsen, T. Nucleic Acids Research, Vol. 35, Issue Database https://doi.org/10.1093/nar/gkl1043	journal	January 2007
CDD: a conserved domain database for interactive domain family analysis Marchler-Bauer, A.; Anderson, J. B.; Derbyshire, M. K. Nucleic Acids Research, Vol. 35, Issue Database https://doi.org/10.1093/nar/gkl951	journal	January 2007
The Pfam protein families database Punta, M.; Coggill, P. C.; Eberhardt, R. Y. Nucleic Acids Research, Vol. 40, Issue D1 https://doi.org/10.1093/nar/gkr1065	journal	November 2011
Data, information, knowledge and principle: back to metabolism in KEGG Kanehisa, Minoru; Goto, Susumu; Sato, Yoko Nucleic Acids Research, Vol. 42, Issue D1 https://doi.org/10.1093/nar/gkt1076	journal	November 2013
The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of Pathway/Genome Databases Caspi, Ron; Altman, Tomer; Billington, Richard Nucleic Acids Research, Vol. 42, Issue D1 https://doi.org/10.1093/nar/gkt1103	journal	November 2013
IMG 4 version of the integrated microbial genomes comparative analysis system Markowitz, Victor M.; Chen, I-Min A.; Palaniappan, Krishna Nucleic Acids Research, Vol. 42, Issue D1 https://doi.org/10.1093/nar/gkt963	journal	October 2013
The Genomes OnLine Database (GOLD) v.5: a metadata management system based on a four level (meta)genome project classification Reddy, T. B. K.; Thomas, Alex D.; Stamatis, Dimitri Nucleic Acids Research, Vol. 43, Issue D1 https://doi.org/10.1093/nar/gku950	journal	October 2014
Prodigal: prokaryotic gene recognition and translation initiation site identification Hyatt, Doug; Chen, Gwo-Liang; LoCascio, Philip F. BMC Bioinformatics, Vol. 11, Issue 1 https://doi.org/10.1186/1471-2105-11-119	journal	March 2010
PILER-CR: Fast and accurate identification of CRISPR repeats Edgar, Robert C. BMC Bioinformatics, Vol. 8, Issue 1 https://doi.org/10.1186/1471-2105-8-18	journal	January 2007
CRISPR Recognition Tool (CRT): a tool for automatic detection of clustered regularly interspaced palindromic repeats Bland, Charles; Ramsey, Teresa L.; Sabree, Fareedah BMC Bioinformatics, Vol. 8, Issue 1 https://doi.org/10.1186/1471-2105-8-209	journal	June 2007
Large-scale contamination of microbial isolate genomes by Illumina PhiX control Mukherjee, Supratim; Huntemann, Marcel; Ivanova, Natalia Standards in Genomic Sciences, Vol. 10, Issue 1 https://doi.org/10.1186/1944-3277-10-18	journal	March 2015
Accelerated Profile HMM Searches Eddy, Sean R. PLoS Computational Biology, Vol. 7, Issue 10 https://doi.org/10.1371/journal.pcbi.1002195	journal	October 2011
Improving Microbial Genome Annotations in an Integrated Database Context Chen, I-Min A.; Markowitz, Victor M.; Chu, Ken PLoS ONE, Vol. 8, Issue 2 https://doi.org/10.1371/journal.pone.0054859	journal	February 2013

Similar Records

The DOE-JGI Standard Operating Procedure for the Annotations of the Microbial Genomes

Journal Article · Wed May 20 00:00:00 EDT 2009 · Standards in Genomic Sciences · OSTI ID:974530

The standard operating procedure of the DOE-JGI Microbial Genome Annotation Pipeline (MGAP v.4)

Citation Formats

References (20)

Similar Records

Related Subjects