EGenBio : a data management system for evolutionary genomics and biodiversity


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dc.contributor.author Nahum, Laila A.
dc.contributor.author Reynolds, Matthew T.
dc.contributor.author Wang, Zhengyuan O.
dc.contributor.author Faith, Jeremiah J.
dc.contributor.author Jonna, Rahul
dc.contributor.author Jiang, Zhi J.
dc.contributor.author Meyer, Thomas J.
dc.contributor.author Pollock, David D.
dc.date.accessioned 2006-10-25T14:01:53Z
dc.date.available 2006-10-25T14:01:53Z
dc.date.issued 2006-09-26
dc.identifier.citation BMC Bioinformatics 7, Suppl 2 (2006) ):S7 en
dc.identifier.uri http://hdl.handle.net/1912/1279
dc.description From The Third Annual Conference of the MidSouth Computational Biology and Bioinformatics Society Baton Rouge, Louisiana. 2–4 March, 2006. en
dc.description © 2006 Nahum et al; licensee BioMed Central Ltd. This is an open access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
dc.description.abstract EGenBio is a system for manipulation and filtering of large numbers of sequences, integrating curated sequence alignments and phylogenetic trees, managing evolutionary analyses, and visualizing their output. EGenBio is organized into three conceptual divisions, Evolution, Genomics, and Biodiversity. The Genomics division includes tools for selecting pre-aligned sequences from different genes and species, and for modifying and filtering these alignments for further analysis. Species searches are handled through queries that can be modified based on a tree-based navigation system and saved. The Biodiversity division contains tools for analyzing individual sequences or sequence alignments, whereas the Evolution division contains tools involving phylogenetic trees. Alignments are annotated with analytical results and modification history using our PRAED format. A miscellaneous Tools section and Help framework are also available. EGenBio was developed around our comparative genomic research and a prototype database of mtDNA genomes. It utilizes MySQL-relational databases and dynamic page generation, and calls numerous custom programs. en
dc.description.sponsorship This work was partly funded by the National Institutes of Health (R22/R33 Innovation and Development grant to David Pollock), the National Science Foundation (CBM2/EPSCOR), and the State of Louisiana (Biological Computation and Visualization Center, Governor's iotechnology Initiative, and startup funds to David Pollock). en
dc.format.extent 358631 bytes
dc.format.mimetype application/pdf
dc.language.iso en en
dc.publisher BioMed Central en
dc.relation.uri http://dx.doi.org/10.1186/1471-2105-7-S2-S7
dc.rights.uri http://creativecommons.org/licenses/by/2.0 *
dc.title EGenBio : a data management system for evolutionary genomics and biodiversity en
dc.type Article en
dc.identifier.doi 10.1186/1471-2105-7-S2-S7

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