Abstract
BackgroundComparative 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.ResultsGenomeBlast 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.ConclusionWe 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 .
Highlights
Comparative genomics has become an essential approach for identifying homologous gene candidates and their functions, and for studying genome evolution
EBV and EHV2 were selected for comparison. 82 homologous coding sequence (CDS) candidates were identified between them
We have developed a Web tool for comparative analysis of small genomes
Summary
Comparative genomics has become an essential approach for identifying homologous gene candidates and their functions, and for studying genome evolution. With the rapidly increasing availability of complete genome sequences, genome-wide sequence comparison has become an essential approach for finding homologous gene candidates, for identifying gene functions, and for studying genome evolution [1,2]. Genome phylogenies based on gene content or gene order shed new light on the construction of the Tree of Life [4,5]. Many tools such as MUMmer and Artemis are available for comparative genomic analysis [2,6,7,8]. Only a few tools can be used for the study of phylogeny from the genomic point of view [13]
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