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

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 subm...

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Autores principales: 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.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2015
Materias:
Standard Operating Procedure
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4623924/
https://www.ncbi.nlm.nih.gov/pubmed/26512311
http://dx.doi.org/10.1186/s40793-015-0077-y
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author 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.
author_facet 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.
author_sort Huntemann, Marcel
collection PubMed
description 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.
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spelling pubmed-46239242015-10-29 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. Stand Genomic Sci Standard Operating Procedure 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. BioMed Central 2015-10-26 /pmc/articles/PMC4623924/ /pubmed/26512311 http://dx.doi.org/10.1186/s40793-015-0077-y Text en © Huntemann et al. 2015 Open AccessThis article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.
spellingShingle Standard Operating Procedure
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.
The standard operating procedure of the DOE-JGI Microbial Genome Annotation Pipeline (MGAP v.4)
title The standard operating procedure of the DOE-JGI Microbial Genome Annotation Pipeline (MGAP v.4)
title_full The standard operating procedure of the DOE-JGI Microbial Genome Annotation Pipeline (MGAP v.4)
title_fullStr The standard operating procedure of the DOE-JGI Microbial Genome Annotation Pipeline (MGAP v.4)
title_full_unstemmed The standard operating procedure of the DOE-JGI Microbial Genome Annotation Pipeline (MGAP v.4)
title_short The standard operating procedure of the DOE-JGI Microbial Genome Annotation Pipeline (MGAP v.4)
title_sort standard operating procedure of the doe-jgi microbial genome annotation pipeline (mgap v.4)
topic Standard Operating Procedure
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4623924/
https://www.ncbi.nlm.nih.gov/pubmed/26512311
http://dx.doi.org/10.1186/s40793-015-0077-y
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