Abstract

Comparative genomics has become an essential approach for identifying homologous gene candidates and their functions, and for studying genome evolution. We developed GenomeBlast, a Web tool for comparative analysis of multiple small genomes. It uses the blastp program for sequence similarity comparison and the maximum parsimony method based on gene content to infer genome phylogeny. Alignment coverage is used to identify global similarity between genes. This strategy takes advantage of the fast BLAST algorithm, and at the same time avoids finding only locally similar sequences but identifies gene-wide similarities (more likely to be homologue candidates). 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; (4) a table of gene presence/absence information and a genome phylogeny. Compared with other similar tools, GenomeBlast is unique in that it integrates all the above functions, and all are easily accessible by the users through a simple Web interface. In this report, we demonstrate the functions included in GenomeBlast with an example of multiple herpes viral genome analysis and how GenomeBlast is useful for small genome comparison

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

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Summary

Introduction

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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