Cargando…
The standard operating procedure of the DOE-JGI Metagenome Annotation Pipeline (MAP v.4)
The DOE-JGI Metagenome Annotation Pipeline (MAP v.4) performs structural and functional annotation for metagenomic sequences that are submitted to the Integrated Microbial Genomes with Microbiomes (IMG/M) system for comparative analysis. The pipeline runs on nucleotide sequences provided via the IMG...
Autores principales: | , , , , , , , , , , , , , |
---|---|
Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
BioMed Central
2016
|
Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4766715/ https://www.ncbi.nlm.nih.gov/pubmed/26918089 http://dx.doi.org/10.1186/s40793-016-0138-x |
_version_ | 1782417718385836032 |
---|---|
author | Huntemann, Marcel Ivanova, Natalia N. Mavromatis, Konstantinos Tripp, H. James Paez-Espino, David Tennessen, Kristin 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 Tennessen, Kristin 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 Metagenome Annotation Pipeline (MAP v.4) performs structural and functional annotation for metagenomic sequences that are submitted to the Integrated Microbial Genomes with Microbiomes (IMG/M) system for comparative analysis. The pipeline runs on nucleotide sequences provided via the IMG submission site. Users must first define their analysis projects in GOLD and then submit the associated sequence datasets consisting of scaffolds/contigs with optional coverage information and/or unassembled reads in fasta and fastq file formats. The MAP processing consists of feature prediction including identification of protein-coding genes, non-coding RNAs and regulatory RNAs, as well as CRISPR elements. Structural annotation is followed by functional annotation including assignment of protein product names and connection to various protein family databases. |
format | Online Article Text |
id | pubmed-4766715 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2016 |
publisher | BioMed Central |
record_format | MEDLINE/PubMed |
spelling | pubmed-47667152016-02-26 The standard operating procedure of the DOE-JGI Metagenome Annotation Pipeline (MAP v.4) Huntemann, Marcel Ivanova, Natalia N. Mavromatis, Konstantinos Tripp, H. James Paez-Espino, David Tennessen, Kristin 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 Metagenome Annotation Pipeline (MAP v.4) performs structural and functional annotation for metagenomic sequences that are submitted to the Integrated Microbial Genomes with Microbiomes (IMG/M) system for comparative analysis. The pipeline runs on nucleotide sequences provided via the IMG submission site. Users must first define their analysis projects in GOLD and then submit the associated sequence datasets consisting of scaffolds/contigs with optional coverage information and/or unassembled reads in fasta and fastq file formats. The MAP processing consists of feature prediction including identification of protein-coding genes, non-coding RNAs and regulatory RNAs, as well as CRISPR elements. Structural annotation is followed by functional annotation including assignment of protein product names and connection to various protein family databases. BioMed Central 2016-02-24 /pmc/articles/PMC4766715/ /pubmed/26918089 http://dx.doi.org/10.1186/s40793-016-0138-x Text en © Huntemann et al. 2016 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 Tennessen, Kristin 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 Metagenome Annotation Pipeline (MAP v.4) |
title | The standard operating procedure of the DOE-JGI Metagenome Annotation Pipeline (MAP v.4) |
title_full | The standard operating procedure of the DOE-JGI Metagenome Annotation Pipeline (MAP v.4) |
title_fullStr | The standard operating procedure of the DOE-JGI Metagenome Annotation Pipeline (MAP v.4) |
title_full_unstemmed | The standard operating procedure of the DOE-JGI Metagenome Annotation Pipeline (MAP v.4) |
title_short | The standard operating procedure of the DOE-JGI Metagenome Annotation Pipeline (MAP v.4) |
title_sort | standard operating procedure of the doe-jgi metagenome annotation pipeline (map v.4) |
topic | Standard Operating Procedure |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4766715/ https://www.ncbi.nlm.nih.gov/pubmed/26918089 http://dx.doi.org/10.1186/s40793-016-0138-x |
work_keys_str_mv | AT huntemannmarcel thestandardoperatingprocedureofthedoejgimetagenomeannotationpipelinemapv4 AT ivanovanatalian thestandardoperatingprocedureofthedoejgimetagenomeannotationpipelinemapv4 AT mavromatiskonstantinos thestandardoperatingprocedureofthedoejgimetagenomeannotationpipelinemapv4 AT tripphjames thestandardoperatingprocedureofthedoejgimetagenomeannotationpipelinemapv4 AT paezespinodavid thestandardoperatingprocedureofthedoejgimetagenomeannotationpipelinemapv4 AT tennessenkristin thestandardoperatingprocedureofthedoejgimetagenomeannotationpipelinemapv4 AT palaniappankrishnaveni thestandardoperatingprocedureofthedoejgimetagenomeannotationpipelinemapv4 AT szetoernest thestandardoperatingprocedureofthedoejgimetagenomeannotationpipelinemapv4 AT pillaymanoj thestandardoperatingprocedureofthedoejgimetagenomeannotationpipelinemapv4 AT chenimina thestandardoperatingprocedureofthedoejgimetagenomeannotationpipelinemapv4 AT patiamrita thestandardoperatingprocedureofthedoejgimetagenomeannotationpipelinemapv4 AT nielsentorben thestandardoperatingprocedureofthedoejgimetagenomeannotationpipelinemapv4 AT markowitzvictorm thestandardoperatingprocedureofthedoejgimetagenomeannotationpipelinemapv4 AT kyrpidesnikosc thestandardoperatingprocedureofthedoejgimetagenomeannotationpipelinemapv4 AT huntemannmarcel standardoperatingprocedureofthedoejgimetagenomeannotationpipelinemapv4 AT ivanovanatalian standardoperatingprocedureofthedoejgimetagenomeannotationpipelinemapv4 AT mavromatiskonstantinos standardoperatingprocedureofthedoejgimetagenomeannotationpipelinemapv4 AT tripphjames standardoperatingprocedureofthedoejgimetagenomeannotationpipelinemapv4 AT paezespinodavid standardoperatingprocedureofthedoejgimetagenomeannotationpipelinemapv4 AT tennessenkristin standardoperatingprocedureofthedoejgimetagenomeannotationpipelinemapv4 AT palaniappankrishnaveni standardoperatingprocedureofthedoejgimetagenomeannotationpipelinemapv4 AT szetoernest standardoperatingprocedureofthedoejgimetagenomeannotationpipelinemapv4 AT pillaymanoj standardoperatingprocedureofthedoejgimetagenomeannotationpipelinemapv4 AT chenimina standardoperatingprocedureofthedoejgimetagenomeannotationpipelinemapv4 AT patiamrita standardoperatingprocedureofthedoejgimetagenomeannotationpipelinemapv4 AT nielsentorben standardoperatingprocedureofthedoejgimetagenomeannotationpipelinemapv4 AT markowitzvictorm standardoperatingprocedureofthedoejgimetagenomeannotationpipelinemapv4 AT kyrpidesnikosc standardoperatingprocedureofthedoejgimetagenomeannotationpipelinemapv4 |