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dc.contributor.authorLu, Guoqingen_US
dc.contributor.authorJiang, Liyingen_US
dc.contributor.authorHelikar, Resa MKen_US
dc.contributor.authorRowley, Thaine Wen_US
dc.contributor.authorZhang, Luwenen_US
dc.contributor.authorChen, Xianfengen_US
dc.contributor.authorMoriyama, Etsuko Nen_US
dc.date.accessioned2012-08-24T12:14:20Z
dc.date.available2012-08-24T12:14:20Z
dc.date.issued2006-12-12en_US
dc.identifier.citationBMC Bioinformatics. 2006 Dec 12;7(Suppl 4):S18en_US
dc.identifier.urihttp://hdl.handle.net/10919/18939
dc.description.abstractBackground 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/.en_US
dc.format.mimetypeapplication/pdfen_US
dc.language.isoen_USen_US
dc.rightsAttribution 4.0 United States*
dc.rights.urihttps://creativecommons.org/licenses/by/4.0/*
dc.titleGenomeBlast: a web tool for small genome comparisonen_US
dc.typeArticle - Refereeden_US
dc.date.updated2012-08-24T12:14:20Z
dc.description.versionPeer Revieweden_US
dc.language.rfc3066enen_US
dc.rights.holderGuoqing Lu et al.; licensee BioMed Central Ltd.en_US
dc.identifier.doihttps://doi.org/10.1186/1471-2105-7-S4-S18
dc.type.dcmitypeTexten_US


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Attribution 4.0 United States
License: Attribution 4.0 United States