MamMiBase: a mitochondrial genome database for mammalian phylogenetic studies
MamMiBase, the mammalian mitochondrial genome database, is a relational database of complete mitochondrial genome sequences of mammalian species. The database is useful for phylogenetic analysis, since it allows a ready retrieval of nucleotide and aminoacid individual alignments, in three different...
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| Veröffentlicht in: | Bioinformatics 2005-05, Vol.21 (10), p.2566-2567 |
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| creator | de Vasconcelos, Ana Tereza R. Guimarães, Ana Carolina R. Castelletti, Carlos Henrique M. Caruso, Célia S. Ribeiro, Cristina Yokaichiya, Fabiano Armôa, Geraldo R. G. Pereira, Gislaine da Silva P. da Silva, Israel T. Schrago, Carlos G. Fernandes, Adélia L. V. da Silveira, Aline R. Carneiro, André G. Carvalho, Bruno M. Viana, Carlos J. M. Gramkow, Daniel Lima, Franklin J. Corrêa, Luiz G. G. Mudado, Maurício de A. Nehab-Hess, Pablo de Souza, Rangel Corrêa, Régis L. Russo, Claudia A. M. |
| description | MamMiBase, the mammalian mitochondrial genome database, is a relational database of complete mitochondrial genome sequences of mammalian species. The database is useful for phylogenetic analysis, since it allows a ready retrieval of nucleotide and aminoacid individual alignments, in three different formats (NEXUS for PAUP program, for MEGA program and for PHYLIP program) of the 13 protein coding mitochondrial genes. The user may download the sequences that are useful for him/her based on their parameters values, such as sequence length, p-distances, base content, transition transversion ratio, gamma, which are also given by MamMiBase. A simple phylogenetic tree (neighbor-joining tree with Jukes Cantor distance) is also available for download, useful for parameter calculations and other simple tasks. Availability: MamMiBase is available at http://www.mammibase.lncc.br Contact: atrv@lncc.br |
| doi_str_mv | 10.1093/bioinformatics/bti326 |
| format | Article |
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G. ; Pereira, Gislaine da Silva P. ; da Silva, Israel T. ; Schrago, Carlos G. ; Fernandes, Adélia L. V. ; da Silveira, Aline R. ; Carneiro, André G. ; Carvalho, Bruno M. ; Viana, Carlos J. M. ; Gramkow, Daniel ; Lima, Franklin J. ; Corrêa, Luiz G. G. ; Mudado, Maurício de A. ; Nehab-Hess, Pablo ; de Souza, Rangel ; Corrêa, Régis L. ; Russo, Claudia A. M.</creator><creatorcontrib>de Vasconcelos, Ana Tereza R. ; Guimarães, Ana Carolina R. ; Castelletti, Carlos Henrique M. ; Caruso, Célia S. ; Ribeiro, Cristina ; Yokaichiya, Fabiano ; Armôa, Geraldo R. G. ; Pereira, Gislaine da Silva P. ; da Silva, Israel T. ; Schrago, Carlos G. ; Fernandes, Adélia L. V. ; da Silveira, Aline R. ; Carneiro, André G. ; Carvalho, Bruno M. ; Viana, Carlos J. M. ; Gramkow, Daniel ; Lima, Franklin J. ; Corrêa, Luiz G. G. ; Mudado, Maurício de A. ; Nehab-Hess, Pablo ; de Souza, Rangel ; Corrêa, Régis L. ; Russo, Claudia A. M.</creatorcontrib><description>MamMiBase, the mammalian mitochondrial genome database, is a relational database of complete mitochondrial genome sequences of mammalian species. The database is useful for phylogenetic analysis, since it allows a ready retrieval of nucleotide and aminoacid individual alignments, in three different formats (NEXUS for PAUP program, for MEGA program and for PHYLIP program) of the 13 protein coding mitochondrial genes. The user may download the sequences that are useful for him/her based on their parameters values, such as sequence length, p-distances, base content, transition transversion ratio, gamma, which are also given by MamMiBase. A simple phylogenetic tree (neighbor-joining tree with Jukes Cantor distance) is also available for download, useful for parameter calculations and other simple tasks. Availability: MamMiBase is available at http://www.mammibase.lncc.br Contact: atrv@lncc.br</description><identifier>ISSN: 1367-4803</identifier><identifier>EISSN: 1460-2059</identifier><identifier>EISSN: 1367-4811</identifier><identifier>DOI: 10.1093/bioinformatics/bti326</identifier><identifier>PMID: 15713730</identifier><identifier>CODEN: BOINFP</identifier><language>eng</language><publisher>Oxford: Oxford University Press</publisher><subject>Biological and medical sciences ; Chromosome Mapping - methods ; Databases, Nucleic Acid ; DNA, Mitochondrial - classification ; DNA, Mitochondrial - genetics ; Fundamental and applied biological sciences. Psychology ; General aspects ; Internet ; Mathematics in biology. Statistical analysis. Models. Metrology. 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G.</creatorcontrib><creatorcontrib>Pereira, Gislaine da Silva P.</creatorcontrib><creatorcontrib>da Silva, Israel T.</creatorcontrib><creatorcontrib>Schrago, Carlos G.</creatorcontrib><creatorcontrib>Fernandes, Adélia L. V.</creatorcontrib><creatorcontrib>da Silveira, Aline R.</creatorcontrib><creatorcontrib>Carneiro, André G.</creatorcontrib><creatorcontrib>Carvalho, Bruno M.</creatorcontrib><creatorcontrib>Viana, Carlos J. M.</creatorcontrib><creatorcontrib>Gramkow, Daniel</creatorcontrib><creatorcontrib>Lima, Franklin J.</creatorcontrib><creatorcontrib>Corrêa, Luiz G. G.</creatorcontrib><creatorcontrib>Mudado, Maurício de A.</creatorcontrib><creatorcontrib>Nehab-Hess, Pablo</creatorcontrib><creatorcontrib>de Souza, Rangel</creatorcontrib><creatorcontrib>Corrêa, Régis L.</creatorcontrib><creatorcontrib>Russo, Claudia A. M.</creatorcontrib><title>MamMiBase: a mitochondrial genome database for mammalian phylogenetic studies</title><title>Bioinformatics</title><addtitle>Bioinformatics</addtitle><description>MamMiBase, the mammalian mitochondrial genome database, is a relational database of complete mitochondrial genome sequences of mammalian species. The database is useful for phylogenetic analysis, since it allows a ready retrieval of nucleotide and aminoacid individual alignments, in three different formats (NEXUS for PAUP program, for MEGA program and for PHYLIP program) of the 13 protein coding mitochondrial genes. The user may download the sequences that are useful for him/her based on their parameters values, such as sequence length, p-distances, base content, transition transversion ratio, gamma, which are also given by MamMiBase. A simple phylogenetic tree (neighbor-joining tree with Jukes Cantor distance) is also available for download, useful for parameter calculations and other simple tasks. Availability: MamMiBase is available at http://www.mammibase.lncc.br Contact: atrv@lncc.br</description><subject>Biological and medical sciences</subject><subject>Chromosome Mapping - methods</subject><subject>Databases, Nucleic Acid</subject><subject>DNA, Mitochondrial - classification</subject><subject>DNA, Mitochondrial - genetics</subject><subject>Fundamental and applied biological sciences. Psychology</subject><subject>General aspects</subject><subject>Internet</subject><subject>Mathematics in biology. Statistical analysis. Models. Metrology. Data processing in biology (general aspects)</subject><subject>Phylogeny</subject><subject>Sequence Alignment - methods</subject><subject>Sequence Analysis, DNA - methods</subject><subject>User-Computer Interface</subject><issn>1367-4803</issn><issn>1460-2059</issn><issn>1367-4811</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2005</creationdate><recordtype>article</recordtype><sourceid>EIF</sourceid><recordid>eNqF0V1rFTEQBuAgiq3Vn6Asgt6tTTL5Wu9s0VbpqSAKxZswm83a1M3mmOyC_fdGzsGiN0IggTyTyfAS8pTRV4x2cNyHFOYx5YhLcOW4XwJwdY8cMqFoy6ns7tczKN0KQ-GAPCrlhlLJhBAPyQGTmoEGekg2G4ybcILFv26wiWFJ7jrNQw44Nd_8nKJvBlywr6Cp3ZqIMeIUcG6217dTqsTX_k1Z1iH48pg8GHEq_sl-PyJf3r39fHreXnw8e3_65qJ19TdL643ghhmHBhTzY9epYdSoOu1Bcl_XIJxRSnWGazFSxjU4Lw30iMwB1XBEXu7e3eb0Y_VlsTEU56cJZ5_WYpU2IBTj_4VMSwVcigqf_wNv0prnOoRlnVGCU60qkjvkciol-9Fuc4iYby2j9ncq9u9U7C6VWvds__jaRz_cVe1jqODFHmBxOI0ZZxfKnVOGS0WhunbnQln8zz_3mL_XkUFLe3711eqTT5dX4uzSfoBfnuipHw</recordid><startdate>20050515</startdate><enddate>20050515</enddate><creator>de Vasconcelos, Ana Tereza R.</creator><creator>Guimarães, Ana Carolina R.</creator><creator>Castelletti, Carlos Henrique M.</creator><creator>Caruso, Célia S.</creator><creator>Ribeiro, Cristina</creator><creator>Yokaichiya, Fabiano</creator><creator>Armôa, Geraldo R. G.</creator><creator>Pereira, Gislaine da Silva P.</creator><creator>da Silva, Israel T.</creator><creator>Schrago, Carlos G.</creator><creator>Fernandes, Adélia L. V.</creator><creator>da Silveira, Aline R.</creator><creator>Carneiro, André G.</creator><creator>Carvalho, Bruno M.</creator><creator>Viana, Carlos J. M.</creator><creator>Gramkow, Daniel</creator><creator>Lima, Franklin J.</creator><creator>Corrêa, Luiz G. G.</creator><creator>Mudado, Maurício de A.</creator><creator>Nehab-Hess, Pablo</creator><creator>de Souza, Rangel</creator><creator>Corrêa, Régis L.</creator><creator>Russo, Claudia A. 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G. ; Pereira, Gislaine da Silva P. ; da Silva, Israel T. ; Schrago, Carlos G. ; Fernandes, Adélia L. V. ; da Silveira, Aline R. ; Carneiro, André G. ; Carvalho, Bruno M. ; Viana, Carlos J. M. ; Gramkow, Daniel ; Lima, Franklin J. ; Corrêa, Luiz G. G. ; Mudado, Maurício de A. ; Nehab-Hess, Pablo ; de Souza, Rangel ; Corrêa, Régis L. ; Russo, Claudia A. M.</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c480t-e842818ca8361ef996df7a697e352e52ed4c866698274f01273ce583baa1c3073</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2005</creationdate><topic>Biological and medical sciences</topic><topic>Chromosome Mapping - methods</topic><topic>Databases, Nucleic Acid</topic><topic>DNA, Mitochondrial - classification</topic><topic>DNA, Mitochondrial - genetics</topic><topic>Fundamental and applied biological sciences. Psychology</topic><topic>General aspects</topic><topic>Internet</topic><topic>Mathematics in biology. Statistical analysis. Models. Metrology. Data processing in biology (general aspects)</topic><topic>Phylogeny</topic><topic>Sequence Alignment - methods</topic><topic>Sequence Analysis, DNA - methods</topic><topic>User-Computer Interface</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>de Vasconcelos, Ana Tereza R.</creatorcontrib><creatorcontrib>Guimarães, Ana Carolina R.</creatorcontrib><creatorcontrib>Castelletti, Carlos Henrique M.</creatorcontrib><creatorcontrib>Caruso, Célia S.</creatorcontrib><creatorcontrib>Ribeiro, Cristina</creatorcontrib><creatorcontrib>Yokaichiya, Fabiano</creatorcontrib><creatorcontrib>Armôa, Geraldo R. 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G.</au><au>Pereira, Gislaine da Silva P.</au><au>da Silva, Israel T.</au><au>Schrago, Carlos G.</au><au>Fernandes, Adélia L. V.</au><au>da Silveira, Aline R.</au><au>Carneiro, André G.</au><au>Carvalho, Bruno M.</au><au>Viana, Carlos J. M.</au><au>Gramkow, Daniel</au><au>Lima, Franklin J.</au><au>Corrêa, Luiz G. G.</au><au>Mudado, Maurício de A.</au><au>Nehab-Hess, Pablo</au><au>de Souza, Rangel</au><au>Corrêa, Régis L.</au><au>Russo, Claudia A. M.</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>MamMiBase: a mitochondrial genome database for mammalian phylogenetic studies</atitle><jtitle>Bioinformatics</jtitle><addtitle>Bioinformatics</addtitle><date>2005-05-15</date><risdate>2005</risdate><volume>21</volume><issue>10</issue><spage>2566</spage><epage>2567</epage><pages>2566-2567</pages><issn>1367-4803</issn><eissn>1460-2059</eissn><eissn>1367-4811</eissn><coden>BOINFP</coden><abstract>MamMiBase, the mammalian mitochondrial genome database, is a relational database of complete mitochondrial genome sequences of mammalian species. The database is useful for phylogenetic analysis, since it allows a ready retrieval of nucleotide and aminoacid individual alignments, in three different formats (NEXUS for PAUP program, for MEGA program and for PHYLIP program) of the 13 protein coding mitochondrial genes. The user may download the sequences that are useful for him/her based on their parameters values, such as sequence length, p-distances, base content, transition transversion ratio, gamma, which are also given by MamMiBase. A simple phylogenetic tree (neighbor-joining tree with Jukes Cantor distance) is also available for download, useful for parameter calculations and other simple tasks. Availability: MamMiBase is available at http://www.mammibase.lncc.br Contact: atrv@lncc.br</abstract><cop>Oxford</cop><pub>Oxford University Press</pub><pmid>15713730</pmid><doi>10.1093/bioinformatics/bti326</doi><tpages>2</tpages><oa>free_for_read</oa></addata></record> |
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| identifier | ISSN: 1367-4803 |
| ispartof | Bioinformatics, 2005-05, Vol.21 (10), p.2566-2567 |
| issn | 1367-4803 1460-2059 1367-4811 |
| language | eng |
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| source | Oxford Journals Open Access Collection; MEDLINE; Elektronische Zeitschriftenbibliothek - Frei zugängliche E-Journals; Alma/SFX Local Collection |
| subjects | Biological and medical sciences Chromosome Mapping - methods Databases, Nucleic Acid DNA, Mitochondrial - classification DNA, Mitochondrial - genetics Fundamental and applied biological sciences. Psychology General aspects Internet Mathematics in biology. Statistical analysis. Models. Metrology. Data processing in biology (general aspects) Phylogeny Sequence Alignment - methods Sequence Analysis, DNA - methods User-Computer Interface |
| title | MamMiBase: a mitochondrial genome database for mammalian phylogenetic studies |
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