Gene context analysis in the Integrated Microbial Genomes (IMG) data management system

Journal Article · Fri May 01 04:00:00 EDT 2009 · PLoS 1

DOI:https://doi.org/10.1371/journal.pone.0007979· OSTI ID:983278

Mavromatis, Konstantinos; Chu, Ken; Ivanova, Natalia; Hooper, Sean D; Markowitz, Victor M; Kyrpides, Nikos C

Computational methods for determining the function of genes in newly sequenced genomes have been traditionally based on sequence similarity to genes whose function has been identified experimentally. Function prediction methods can be extended using gene context analysis approaches such as examining the conservation of chromosomal gene clusters, gene fusion events and co-occurrence profiles across genomes. Context analysis is based on the observation that functionally related genes are often having similar gene context and relies on the identification of such events across a statistically significant and phylogeneticaly diverse collection of genomes. We have used the data management system of the Integrated Microbial Genomes (IMG) as the framework to implement and explore the power of gene context analysis methods because it provides one of the largest available genome integrations. Visualization and search tools to facilitate and explore gene context analysis have been developed and applied across all publicly available archaeal and bacterial genomes in IMG. These computations are now maintained as part of IMG's regular genome content update cycle. IMG is available at: http://img.jgi.doe.gov.

• Research Organization: Ernest Orlando Lawrence Berkeley National Laboratory, Berkeley, CA (US)
• Sponsoring Organization: Genomics Division
• DOE Contract Number: AC02-05CH11231
• OSTI ID: 983278
• Report Number(s): LBNL-3478E
• Journal Information: PLoS 1, Journal Name: PLoS 1
• Country of Publication: United States
• Language: English

Related Subjects

59 BASIC BIOLOGICAL SCIENCES
FORECASTING
GENES
MANAGEMENT