Bioinformatics Advance Access originally published online on July 22, 2004
Bioinformatics 2004 20(18):3462-3465; doi:10.1093/bioinformatics/bth427
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Bioinformatics vol. 20 issue 18 © Oxford University Press 2004; all rights reserved.
ORFcurator: molecular curation of genes and gene clusters in prokaryotic organisms
1 Division of Invertebrate Zoology, Central Park West, 79th Street, American Museum of Natural History, New York, NY 10024, USA, 2 Department of Biomedical Informatics and 3 Department of Microbiology, College of Physicians and Surgeons, Columbia University, New York, NY USA
Received on April 15, 2004; revised on June 2, 2004; accepted on July 16, 2004
Advance Access Publication July 22, 2004
Summary: The ability to detect clusters of functionally related genes in multiple microbial genomes has enormous potential for enhancing studies on gene function and microbial evolution. The staggering amount of new genome sequence data presents a largely untapped resource for gene cluster discovery. To date, gene cluster analysis has not been fully automated, and one must rely on manual, tedious and time-consuming manipulation of sequences. To facilitate accurate and rapid identification of conserved gene clusters, we developed a database-driven web application, called ORFcurator. We used ORFcurator to find clusters containing any genes similar to those of the 14-gene Widespread Colonization Island of Actinobacillus actinomycetemcomitans. From 126 genomes, ORFcurator identified all 73 clusters previously determined by manual searching.
Availability: ORFcurator and all associated scripts are freely available as supplementary information.
Supplementary information: http://www.genomecurator.org/ORFcurator/
Contact: desalle{at}amnh.org
* To whom correspondence should be addressed.
The authors wish it to be known that, in their opinion, the first two authors should be regarded as joint First Authors.
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