GenomeBlast

A Web tool for small genome comparison

Guoqing Lu, Liying Jiang, Resa M. Kotalik, Thaine W. Rowley, Luwen Zhang, Xianfeng Chen, Etsuko Moriyama

Research output: Chapter in Book/Report/Conference proceedingConference contribution

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 outer 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.

Original languageEnglish (US)
Title of host publicationFirst International Multi- Symposiums on Computer and Computational Sciences, IMSCCS'06
Pages136-141
Number of pages6
DOIs
StatePublished - Dec 22 2006
EventFirst International Multi- Symposiums on Computer and Computational Sciences, IMSCCS'06 - Hangzhou, Zhejiang, China
Duration: Apr 20 2006Apr 24 2006

Publication series

NameFirst International Multi- Symposiums on Computer and Computational Sciences, IMSCCS'06
Volume1

Conference

ConferenceFirst International Multi- Symposiums on Computer and Computational Sciences, IMSCCS'06
CountryChina
CityHangzhou, Zhejiang
Period4/20/064/24/06

Fingerprint

Genes

ASJC Scopus subject areas

  • Engineering(all)

Cite this

Lu, G., Jiang, L., Kotalik, R. M., Rowley, T. W., Zhang, L., Chen, X., & Moriyama, E. (2006). GenomeBlast: A Web tool for small genome comparison. In First International Multi- Symposiums on Computer and Computational Sciences, IMSCCS'06 (pp. 136-141). [1636030] (First International Multi- Symposiums on Computer and Computational Sciences, IMSCCS'06; Vol. 1). https://doi.org/10.1109/IMSCCS.2006.71

GenomeBlast : A Web tool for small genome comparison. / Lu, Guoqing; Jiang, Liying; Kotalik, Resa M.; Rowley, Thaine W.; Zhang, Luwen; Chen, Xianfeng; Moriyama, Etsuko.

First International Multi- Symposiums on Computer and Computational Sciences, IMSCCS'06. 2006. p. 136-141 1636030 (First International Multi- Symposiums on Computer and Computational Sciences, IMSCCS'06; Vol. 1).

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Lu, G, Jiang, L, Kotalik, RM, Rowley, TW, Zhang, L, Chen, X & Moriyama, E 2006, GenomeBlast: A Web tool for small genome comparison. in First International Multi- Symposiums on Computer and Computational Sciences, IMSCCS'06., 1636030, First International Multi- Symposiums on Computer and Computational Sciences, IMSCCS'06, vol. 1, pp. 136-141, First International Multi- Symposiums on Computer and Computational Sciences, IMSCCS'06, Hangzhou, Zhejiang, China, 4/20/06. https://doi.org/10.1109/IMSCCS.2006.71
Lu G, Jiang L, Kotalik RM, Rowley TW, Zhang L, Chen X et al. GenomeBlast: A Web tool for small genome comparison. In First International Multi- Symposiums on Computer and Computational Sciences, IMSCCS'06. 2006. p. 136-141. 1636030. (First International Multi- Symposiums on Computer and Computational Sciences, IMSCCS'06). https://doi.org/10.1109/IMSCCS.2006.71
Lu, Guoqing ; Jiang, Liying ; Kotalik, Resa M. ; Rowley, Thaine W. ; Zhang, Luwen ; Chen, Xianfeng ; Moriyama, Etsuko. / GenomeBlast : A Web tool for small genome comparison. First International Multi- Symposiums on Computer and Computational Sciences, IMSCCS'06. 2006. pp. 136-141 (First International Multi- Symposiums on Computer and Computational Sciences, IMSCCS'06).
@inproceedings{a5a3c77ef63b46a39c015feade6f8d37,
title = "GenomeBlast: A Web tool for small genome comparison",
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 outer 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.",
author = "Guoqing Lu and Liying Jiang and Kotalik, {Resa M.} and Rowley, {Thaine W.} and Luwen Zhang and Xianfeng Chen and Etsuko Moriyama",
year = "2006",
month = "12",
day = "22",
doi = "10.1109/IMSCCS.2006.71",
language = "English (US)",
isbn = "0769525814",
series = "First International Multi- Symposiums on Computer and Computational Sciences, IMSCCS'06",
pages = "136--141",
booktitle = "First International Multi- Symposiums on Computer and Computational Sciences, IMSCCS'06",

}

TY - GEN

T1 - GenomeBlast

T2 - A Web tool for small genome comparison

AU - Lu, Guoqing

AU - Jiang, Liying

AU - Kotalik, Resa M.

AU - Rowley, Thaine W.

AU - Zhang, Luwen

AU - Chen, Xianfeng

AU - Moriyama, Etsuko

PY - 2006/12/22

Y1 - 2006/12/22

N2 - 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 outer 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.

AB - 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 outer 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.

UR - http://www.scopus.com/inward/record.url?scp=33845564336&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=33845564336&partnerID=8YFLogxK

U2 - 10.1109/IMSCCS.2006.71

DO - 10.1109/IMSCCS.2006.71

M3 - Conference contribution

SN - 0769525814

SN - 9780769525815

T3 - First International Multi- Symposiums on Computer and Computational Sciences, IMSCCS'06

SP - 136

EP - 141

BT - First International Multi- Symposiums on Computer and Computational Sciences, IMSCCS'06

ER -