GenomeBlast: a web tool for small genome comparison

Lu, Guoqing; Jiang, Liying; Helikar, Resa M. K.; Rowley, Thaine W.; Zhang, Luwen; Chen, Xianfeng; Moriyama, Etsuko N.

GenomeBlast: a web tool for small genome comparison

dc.contributor.author	Lu, Guoqing	en
dc.contributor.author	Jiang, Liying	en
dc.contributor.author	Helikar, Resa M. K.	en
dc.contributor.author	Rowley, Thaine W.	en
dc.contributor.author	Zhang, Luwen	en
dc.contributor.author	Chen, Xianfeng	en
dc.contributor.author	Moriyama, Etsuko N.	en
dc.date.accessioned	2012-08-24T12:14:20Z	en
dc.date.available	2012-08-24T12:14:20Z	en
dc.date.issued	2006-12-12	en
dc.date.updated	2012-08-24T12:14:20Z	en
dc.description.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/.	en
dc.description.version	Published version	en
dc.format.mimetype	application/pdf	en
dc.identifier.citation	BMC Bioinformatics. 2006 Dec 12;7(Suppl 4):S18	en
dc.identifier.doi	https://doi.org/10.1186/1471-2105-7-S4-S18	en
dc.identifier.uri	http://hdl.handle.net/10919/18939	en
dc.language.iso	en	en
dc.rights	Creative Commons Attribution 4.0 International	en
dc.rights.holder	Guoqing Lu et al.; licensee BioMed Central Ltd.	en
dc.rights.uri	http://creativecommons.org/licenses/by/4.0/	en
dc.title	GenomeBlast: a web tool for small genome comparison	en
dc.title.serial	BMC Bioinformatics	en
dc.type	Article - Refereed	en
dc.type.dcmitype	Text	en