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TheViral MetaGenome Annotation Pipeline(VMGAP):an automated tool for the functional annotation of viral Metagenomic shotgun sequencing data

In the past few years, the field of metagenomics has been growing at an accelerated pace, particularly in response to advancements in new sequencing technologies. The large volume of sequence data from novel organisms generated by metagenomic projects has triggered the development of specialized dat...

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Autores principales: Lorenzi, Hernan A., Hoover, Jeff, Inman, Jason, Safford, Todd, Murphy, Sean, Kagan, Leonid, Williamson, Shannon J.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Michigan State University 2011
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3156399/
https://www.ncbi.nlm.nih.gov/pubmed/21886867
http://dx.doi.org/10.4056/sigs.1694706
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author Lorenzi, Hernan A.
Hoover, Jeff
Inman, Jason
Safford, Todd
Murphy, Sean
Kagan, Leonid
Williamson, Shannon J.
author_facet Lorenzi, Hernan A.
Hoover, Jeff
Inman, Jason
Safford, Todd
Murphy, Sean
Kagan, Leonid
Williamson, Shannon J.
author_sort Lorenzi, Hernan A.
collection PubMed
description In the past few years, the field of metagenomics has been growing at an accelerated pace, particularly in response to advancements in new sequencing technologies. The large volume of sequence data from novel organisms generated by metagenomic projects has triggered the development of specialized databases and tools focused on particular groups of organisms or data types. Here we describe a pipeline for the functional annotation of viral metagenomic sequence data. The Viral MetaGenome Annotation Pipeline (VMGAP) pipeline takes advantage of a number of specialized databases, such as collections of mobile genetic elements and environmental metagenomes to improve the classification and functional prediction of viral gene products. The pipeline assigns a functional term to each predicted protein sequence following a suite of comprehensive analyses whose results are ranked according to a priority rules hierarchy. Additional annotation is provided in the form of enzyme commission (EC) numbers, GO/MeGO terms and Hidden Markov Models together with supporting evidence.
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spelling pubmed-31563992011-08-31 TheViral MetaGenome Annotation Pipeline(VMGAP):an automated tool for the functional annotation of viral Metagenomic shotgun sequencing data Lorenzi, Hernan A. Hoover, Jeff Inman, Jason Safford, Todd Murphy, Sean Kagan, Leonid Williamson, Shannon J. Stand Genomic Sci Standard Operating Procedures In the past few years, the field of metagenomics has been growing at an accelerated pace, particularly in response to advancements in new sequencing technologies. The large volume of sequence data from novel organisms generated by metagenomic projects has triggered the development of specialized databases and tools focused on particular groups of organisms or data types. Here we describe a pipeline for the functional annotation of viral metagenomic sequence data. The Viral MetaGenome Annotation Pipeline (VMGAP) pipeline takes advantage of a number of specialized databases, such as collections of mobile genetic elements and environmental metagenomes to improve the classification and functional prediction of viral gene products. The pipeline assigns a functional term to each predicted protein sequence following a suite of comprehensive analyses whose results are ranked according to a priority rules hierarchy. Additional annotation is provided in the form of enzyme commission (EC) numbers, GO/MeGO terms and Hidden Markov Models together with supporting evidence. Michigan State University 2011-06-30 /pmc/articles/PMC3156399/ /pubmed/21886867 http://dx.doi.org/10.4056/sigs.1694706 Text en http://creativecommons.org/licenses/by/2.5/ This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Standard Operating Procedures
Lorenzi, Hernan A.
Hoover, Jeff
Inman, Jason
Safford, Todd
Murphy, Sean
Kagan, Leonid
Williamson, Shannon J.
TheViral MetaGenome Annotation Pipeline(VMGAP):an automated tool for the functional annotation of viral Metagenomic shotgun sequencing data
title TheViral MetaGenome Annotation Pipeline(VMGAP):an automated tool for the functional annotation of viral Metagenomic shotgun sequencing data
title_full TheViral MetaGenome Annotation Pipeline(VMGAP):an automated tool for the functional annotation of viral Metagenomic shotgun sequencing data
title_fullStr TheViral MetaGenome Annotation Pipeline(VMGAP):an automated tool for the functional annotation of viral Metagenomic shotgun sequencing data
title_full_unstemmed TheViral MetaGenome Annotation Pipeline(VMGAP):an automated tool for the functional annotation of viral Metagenomic shotgun sequencing data
title_short TheViral MetaGenome Annotation Pipeline(VMGAP):an automated tool for the functional annotation of viral Metagenomic shotgun sequencing data
title_sort theviral metagenome annotation pipeline(vmgap):an automated tool for the functional annotation of viral metagenomic shotgun sequencing data
topic Standard Operating Procedures
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3156399/
https://www.ncbi.nlm.nih.gov/pubmed/21886867
http://dx.doi.org/10.4056/sigs.1694706
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