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

Journal Article · Fri Aug 05 00:00:00 EDT 2011 · BMC Bioinformatics

DOI:https://doi.org/10.1186/1471-2105-12-S7-A9· OSTI ID:1629376

Aziz, Ramy K. ^[1]; Dwivedi, Bhakti ^[2]; Breitbart, Mya ^[2]; Edwards, Robert A. ^[3]

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1. San Diego State Univ., CA (United States). Dept. of Computer Science; Cairo Univ. (Egypt)
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)

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)
• Grant/Contract Number: DBI-0850356; DBI-0850206
• OSTI ID: 1629376
• Journal Information: BMC Bioinformatics, Vol. 12, Issue S7; Conference: 10.Annual UT-ORNL-KBRIN Bioinformatics Summit 2011, Memphis, TN (United States), 1-3 Apr 2011; ISSN 1471-2105
• Publisher: BioMed Central
• Country of Publication: United States
• Language: English

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59 BASIC BIOLOGICAL SCIENCES