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.

doi:10.4056/sigs.1694706

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

Journal Article · Thu Jun 30 00:00:00 EDT 2011 · Standards in Genomic Sciences

DOI:https://doi.org/10.4056/sigs.1694706· OSTI ID:1628653

Lorenzi, Hernan A. ^[1]; Hoover, Jeff ^[2]; Inman, Jason ^[2]; Safford, Todd ^[2]; Murphy, Sean ^[2]; Kagan, Leonid ^[2]; Williamson, Shannon J. ^[2]

J. Craig Venter Inst., Inc., Rockville, MD (United States); DOE/OSTI
J. Craig Venter Inst., Inc., Rockville, MD (United States)

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.

View Accepted Manuscript (DOE)

Research Organization:: J. Craig Venter Inst., Inc., Rockville, MD (United States)

Sponsoring Organization:: USDOE Office of Science (SC)

Grant/Contract Number:: FC02-02ER63453

OSTI ID:: 1628653

Journal Information:: Standards in Genomic Sciences, Journal Name: Standards in Genomic Sciences Journal Issue: 3 Vol. 4; ISSN 1944-3277

Publisher:: BioMed CentralCopyright Statement

Country of Publication:: United States

Language:: English

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59 BASIC BIOLOGICAL SCIENCES
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J. Craig Venter Institute
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TheViral MetaGenome Annotation Pipeline (VMGAP):an automated tool for the functional annotation of viral Metagenomic shotgun sequencing data

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