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Phage Eco-Locator: a web tool for visualization and analysis of phage genomes in metagenomic data sets

Journal Article · · BMC Bioinformatics
 [1];  [2];  [2];  [3]
  1. San Diego State Univ., CA (United States). Dept. of Computer Science; Cairo Univ. (Egypt); DOE/OSTI
  2. Univ. of South Florida, St. Petersburg, FL (United States). College of Marine Science
  3. San Diego State Univ., CA (United States). Dept. of Computer Science; Argonne National Lab. (ANL), Argonne, IL (United States)
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Bacteriophages, viruses that infect bacteria, are the most abundant biological entities on our planet, and their nucleic acids constitute a substantial proportion of total DNA in Earth’s ecosystems. While the advent of metagenomic methods has allowed the rapid and efficient investigation of microbial and viral communities, there has not been a comprehensive comparative analysis of phage genes and genomes present in all sequenced ecosystems. To examine the abundance and distribution of phage genes in environmental metagenomic sequences, we developed a web-based tool, Phage Eco-Locator [http://www.phantome.org/eco-locator] that screens all publicly available sequenced metagenomes for a user-defined phage genome, or all phage genomes within a user-selected metagenomic sample.

Research Organization:
Argonne National Laboratory (ANL), Argonne, IL (United States)
Sponsoring Organization:
USDOE Office of Science (SC), Biological and Environmental Research (BER); National Science Foundation (NSF)
OSTI ID:
1629376
Journal Information:
BMC Bioinformatics, Journal Name: BMC Bioinformatics Journal Issue: S7 Vol. 12; ISSN 1471-2105
Publisher:
BioMed CentralCopyright Statement
Country of Publication:
United States
Language:
English

References (8)

Phage Metagenomics book January 2007
Here a virus, there a virus, everywhere the same virus? journal June 2005
Functional viral metagenomics and the next generation of molecular tools journal January 2010
High abundance of viruses found in aquatic environments journal August 1989
Viral metagenomics journal May 2005
Gapped BLAST and PSI-BLAST: a new generation of protein database search programs journal September 1997
Gene Transfer by Transduction in the Marine Environment journal August 1998
Metagenomics: Application of Genomics to Uncultured Microorganisms journal December 2004

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Related Subjects

59 BASIC BIOLOGICAL SCIENCES