GeneclusterViz: a tool for conserved gene cluster visualization, exploration and analysis
Gene clusters are arrangements of functionally related genes on a chromosome. In bacteria, it is expected that evolutionary pressures would conserve these arrangements due to the functional advantages they provide. Visualization of conserved gene clusters across multiple genomes provides key insight...
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| Veröffentlicht in: | Bioinformatics (Oxford, England) England), 2012-06, Vol.28 (11), p.1527-1529 |
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| creator | PEJAVER, Vikas R AN, Jaehyun KIM, Sun RHEE, Sungmin BHAN, Ankita CHOI, Jeong-Hyeon BOSHU LIU LEE, Heewook BROWN, Pamela J KYSELA, David BRUN, Yves V |
| description | Gene clusters are arrangements of functionally related genes on a chromosome. In bacteria, it is expected that evolutionary pressures would conserve these arrangements due to the functional advantages they provide. Visualization of conserved gene clusters across multiple genomes provides key insights into their evolutionary histories. Therefore, a software tool that enables visualization and functional analyses of gene clusters would be a great asset to the biological research community.
We have developed GeneclusterViz, a Java-based tool that allows for the visualization, exploration and downstream analyses of conserved gene clusters across multiple genomes. GeneclusterViz combines an easy-to-use exploration interface for gene clusters with a host of other analysis features such as multiple sequence alignments, phylogenetic analyses and integration with the KEGG pathway database.
http://biohealth.snu.ac.kr/GeneclusterViz/; http://microbial.informatics.indiana.edu/GeneclusterViz/ |
| doi_str_mv | 10.1093/bioinformatics/bts177 |
| format | Article |
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We have developed GeneclusterViz, a Java-based tool that allows for the visualization, exploration and downstream analyses of conserved gene clusters across multiple genomes. GeneclusterViz combines an easy-to-use exploration interface for gene clusters with a host of other analysis features such as multiple sequence alignments, phylogenetic analyses and integration with the KEGG pathway database.
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We have developed GeneclusterViz, a Java-based tool that allows for the visualization, exploration and downstream analyses of conserved gene clusters across multiple genomes. GeneclusterViz combines an easy-to-use exploration interface for gene clusters with a host of other analysis features such as multiple sequence alignments, phylogenetic analyses and integration with the KEGG pathway database.
http://biohealth.snu.ac.kr/GeneclusterViz/; http://microbial.informatics.indiana.edu/GeneclusterViz/</description><subject>Alphaproteobacteria - classification</subject><subject>Alphaproteobacteria - genetics</subject><subject>Applications Note</subject><subject>Biological and medical sciences</subject><subject>Cluster Analysis</subject><subject>Escherichia coli - genetics</subject><subject>Fundamental and applied biological sciences. Psychology</subject><subject>General aspects</subject><subject>Genome</subject><subject>Mathematics in biology. Statistical analysis. Models. Metrology. Data processing in biology (general aspects)</subject><subject>Multigene Family</subject><subject>Phylogeny</subject><subject>Sequence Alignment</subject><subject>Software</subject><issn>1367-4803</issn><issn>1367-4811</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2012</creationdate><recordtype>article</recordtype><sourceid>EIF</sourceid><recordid>eNpVkU9rVDEUxYNUbDv6EZRsCi46nfx9yeuiIKXWQsGNCq5CJi-pkUwyzX1vaPvpjc442sUlN8nvnHvhIPSWkjNKer5YxhJzKHVlx-hgsRyBKvUCHVHeqbnQlB7se8IP0THAT0KIJLJ7hQ4ZE71Ukh2h79c-e5cmGH39Fp_OscVjKQk3Z-xKBl83fsB3DcI7Cm8iTDbFpza45FPsH9ap1D8XbPPQyqZHiPAavQw2gX-zO2fo68erL5ef5refr28uP9zOnRB0nAdFqZO9lGxJaVtPecEEV8QT3XeKha499SwM2uoQhAwNoswLoYbecycGPkMXW9_1tFz5wfk8VpvMusaVrY-m2Gie_-T4w9yVjeFcdlqwZvB-Z1DL_eRhNKsIzqdksy8TGEqoFJ3WHWmo3KKuFoDqw34MJeZ3LOZ5LGYbS9O9-3_HvepvDg042QEWnE2h2uwi_OOk7rnWnP8CWGydfw</recordid><startdate>20120601</startdate><enddate>20120601</enddate><creator>PEJAVER, Vikas R</creator><creator>AN, Jaehyun</creator><creator>KIM, Sun</creator><creator>RHEE, Sungmin</creator><creator>BHAN, Ankita</creator><creator>CHOI, Jeong-Hyeon</creator><creator>BOSHU LIU</creator><creator>LEE, Heewook</creator><creator>BROWN, Pamela J</creator><creator>KYSELA, David</creator><creator>BRUN, Yves V</creator><general>Oxford University Press</general><scope>IQODW</scope><scope>CGR</scope><scope>CUY</scope><scope>CVF</scope><scope>ECM</scope><scope>EIF</scope><scope>NPM</scope><scope>AAYXX</scope><scope>CITATION</scope><scope>7X8</scope><scope>5PM</scope></search><sort><creationdate>20120601</creationdate><title>GeneclusterViz: a tool for conserved gene cluster visualization, exploration and analysis</title><author>PEJAVER, Vikas R ; AN, Jaehyun ; KIM, Sun ; RHEE, Sungmin ; BHAN, Ankita ; CHOI, Jeong-Hyeon ; BOSHU LIU ; LEE, Heewook ; BROWN, Pamela J ; KYSELA, David ; BRUN, Yves V</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c441t-f711c59552b115057e424370e089672f605792fd8a8ff45f11512e447d9e3c4d3</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2012</creationdate><topic>Alphaproteobacteria - classification</topic><topic>Alphaproteobacteria - genetics</topic><topic>Applications Note</topic><topic>Biological and medical sciences</topic><topic>Cluster Analysis</topic><topic>Escherichia coli - genetics</topic><topic>Fundamental and applied biological sciences. Psychology</topic><topic>General aspects</topic><topic>Genome</topic><topic>Mathematics in biology. Statistical analysis. Models. Metrology. 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In bacteria, it is expected that evolutionary pressures would conserve these arrangements due to the functional advantages they provide. Visualization of conserved gene clusters across multiple genomes provides key insights into their evolutionary histories. Therefore, a software tool that enables visualization and functional analyses of gene clusters would be a great asset to the biological research community.
We have developed GeneclusterViz, a Java-based tool that allows for the visualization, exploration and downstream analyses of conserved gene clusters across multiple genomes. GeneclusterViz combines an easy-to-use exploration interface for gene clusters with a host of other analysis features such as multiple sequence alignments, phylogenetic analyses and integration with the KEGG pathway database.
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| ispartof | Bioinformatics (Oxford, England), 2012-06, Vol.28 (11), p.1527-1529 |
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| source | MEDLINE; Access via Oxford University Press (Open Access Collection); EZB-FREE-00999 freely available EZB journals; PubMed Central; Alma/SFX Local Collection |
| subjects | Alphaproteobacteria - classification Alphaproteobacteria - genetics Applications Note Biological and medical sciences Cluster Analysis Escherichia coli - genetics Fundamental and applied biological sciences. Psychology General aspects Genome Mathematics in biology. Statistical analysis. Models. Metrology. Data processing in biology (general aspects) Multigene Family Phylogeny Sequence Alignment Software |
| title | GeneclusterViz: a tool for conserved gene cluster visualization, exploration and analysis |
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