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This article is part of the supplement: Symposium of Computations in Bioinformatics and Bioscience (SCBB06)

Open Access Research

GenomeBlast: a web tool for small genome comparison

Guoqing Lu15*, Liying Jiang2, Resa MK Helikar3, Thaine W Rowley3, Luwen Zhang45, Xianfeng Chen6 and Etsuko N Moriyama47

Author Affiliations

1 Department of Biology, University of Nebraska at Omaha, Omaha, NE 68182, USA

2 Department of Computer Science, University of Nebraska-Lincoln, Lincoln, NE 68588, USA

3 Department of Computer Science, University of Nebraska at Omaha, Omaha, NE 68182, USA

4 School of Biological Sciences, University of Nebraska-Lincoln, Lincoln, NE 68588, USA

5 Nebraska Center for Virology, University of Nebraska-Lincoln, Lincoln, NE 68588, USA

6 Virginia Bioinformatics Institute, Virginia Tech Blacksburg, VA 24061, USA

7 Plant Science Initiative, University of Nebraska-Lincoln, Lincoln, NE 68588, USA

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BMC Bioinformatics 2006, 7(Suppl 4):S18  doi:10.1186/1471-2105-7-S4-S18

Published: 12 December 2006

Abstract

Background

Comparative genomics has become an essential approach for identifying homologous gene candidates and their functions, and for studying genome evolution. There are many tools available for genome comparisons. Unfortunately, most of them are not applicable for the identification of unique genes and the inference of phylogenetic relationships in a given set of genomes.

Results

GenomeBlast is a Web tool developed for comparative analysis of multiple small genomes. A new parameter called "coverage" was introduced and used along with sequence identity to evaluate global similarity between genes. With GenomeBlast, the following results can be obtained: (1) unique genes in each genome; (2) homologous gene candidates among compared genomes; (3) 2D plots of homologous gene candidates along the all pairwise genome comparisons; and (4) a table of gene presence/absence information and a genome phylogeny. We demonstrated the functions in GenomeBlast with an example of multiple herpesviral genome analysis and illustrated how GenomeBlast is useful for small genome comparison.

Conclusion

We developed a Web tool for comparative analysis of small genomes, which allows the user not only to identify unique genes and homologous gene candidates among multiple genomes, but also to view their graphical distributions on genomes, and to reconstruct genome phylogeny. GenomeBlast runs on a Linux server with 4 CPUs and 4 GB memory. The online version of GenomeBlast is available to public by using a Web browser with the URL http://bioinfo-srv1.awh.unomaha.edu/genomeblast/ webcite.