Detecting sequence homology at the gene cluster level with multigeneblast

Marnix H. Medema; Eriko Takano; Rainer Breitling

doi:10.1093/molbev/mst025

Detecting sequence homology at the gene cluster level with multigeneblast

Marnix H. Medema, Eriko Takano, Rainer Breitling

Research output: Contribution to journal › Article › peer-review

Abstract

The genes encoding many biomolecular systems and pathways are genomically organized in operons or gene clusters. With MultiGeneBlast, we provide a user-friendly and effective tool to perform homology searches with operons or gene clusters as basic units, instead of single genes. The contextualization offered by MultiGeneBlast allows users to get a better understanding of the function, evolutionary history, and practical applications of such genomic regions. The tool is fully equipped with applications to generate search databases from GenBank or from the user's own sequence data. Finally, an architecture search mode allows searching for gene clusters with novel configurations, by detecting genomic regions with any user-specified combination of genes. Sources, precompiled binaries, and a graphical tutorial of MultiGeneBlast are freely available from http://multigeneblast.sourceforge.net/. © 2013 The Author.

Original language	English
Pages (from-to)	1218-1223
Number of pages	5
Journal	Molecular Biology and Evolution
Volume	30
Issue number	5
DOIs	https://doi.org/10.1093/molbev/mst025
Publication status	Published - May 2013

Keywords

comparative genomics
evolution
gene clusters
homology
operons
software

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title = "Detecting sequence homology at the gene cluster level with multigeneblast",

abstract = "The genes encoding many biomolecular systems and pathways are genomically organized in operons or gene clusters. With MultiGeneBlast, we provide a user-friendly and effective tool to perform homology searches with operons or gene clusters as basic units, instead of single genes. The contextualization offered by MultiGeneBlast allows users to get a better understanding of the function, evolutionary history, and practical applications of such genomic regions. The tool is fully equipped with applications to generate search databases from GenBank or from the user's own sequence data. Finally, an architecture search mode allows searching for gene clusters with novel configurations, by detecting genomic regions with any user-specified combination of genes. Sources, precompiled binaries, and a graphical tutorial of MultiGeneBlast are freely available from http://multigeneblast.sourceforge.net/. {\textcopyright} 2013 The Author.",

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T1 - Detecting sequence homology at the gene cluster level with multigeneblast

AU - Medema, Marnix H.

AU - Takano, Eriko

AU - Breitling, Rainer

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N2 - The genes encoding many biomolecular systems and pathways are genomically organized in operons or gene clusters. With MultiGeneBlast, we provide a user-friendly and effective tool to perform homology searches with operons or gene clusters as basic units, instead of single genes. The contextualization offered by MultiGeneBlast allows users to get a better understanding of the function, evolutionary history, and practical applications of such genomic regions. The tool is fully equipped with applications to generate search databases from GenBank or from the user's own sequence data. Finally, an architecture search mode allows searching for gene clusters with novel configurations, by detecting genomic regions with any user-specified combination of genes. Sources, precompiled binaries, and a graphical tutorial of MultiGeneBlast are freely available from http://multigeneblast.sourceforge.net/. © 2013 The Author.

AB - The genes encoding many biomolecular systems and pathways are genomically organized in operons or gene clusters. With MultiGeneBlast, we provide a user-friendly and effective tool to perform homology searches with operons or gene clusters as basic units, instead of single genes. The contextualization offered by MultiGeneBlast allows users to get a better understanding of the function, evolutionary history, and practical applications of such genomic regions. The tool is fully equipped with applications to generate search databases from GenBank or from the user's own sequence data. Finally, an architecture search mode allows searching for gene clusters with novel configurations, by detecting genomic regions with any user-specified combination of genes. Sources, precompiled binaries, and a graphical tutorial of MultiGeneBlast are freely available from http://multigeneblast.sourceforge.net/. © 2013 The Author.

KW - comparative genomics

KW - evolution

KW - gene clusters

KW - homology

KW - operons

KW - software

U2 - 10.1093/molbev/mst025

DO - 10.1093/molbev/mst025

M3 - Article

SN - 1537-1719

VL - 30

SP - 1218

EP - 1223

JO - Molecular Biology and Evolution

JF - Molecular Biology and Evolution

IS - 5

ER -

Detecting sequence homology at the gene cluster level with multigeneblast

Abstract

Keywords

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