EGenBio: A Data Management System for Evolutionary Genomics and Biodiversity

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dc.contributor.author Nahum, Laila A en_US
dc.contributor.author Reynolds, Matthew T en_US
dc.contributor.author Wang, Zhengyuan O en_US
dc.contributor.author Faith, Jeremiah J en_US
dc.contributor.author Jonna, Rahul en_US
dc.contributor.author Jiang, Zhi J en_US
dc.contributor.author Meyer, Thomas J en_US
dc.contributor.author Pollock, David D en_US
dc.date.accessioned 2012-01-11T21:09:34Z
dc.date.available 2012-01-11T21:09:34Z
dc.date.copyright 2006 en_US
dc.date.issued 2006-9-26 en_US
dc.identifier.citation Nahum, Laila A, Matthew T Reynolds, Zhengyuan O Wang, Jeremiah J Faith, Rahul Jonna, Zhi J Jiang, Thomas J Meyer, David D Pollock. "EGenBio: A Data Management System for Evolutionary Genomics and Biodiversity" BMC Bioinformatics 7(Suppl 2):S7. (2006) en_US
dc.identifier.issn 1471-2105 en_US
dc.identifier.uri http://hdl.handle.net/2144/3194
dc.description.abstract BACKGROUND. Evolutionary genomics requires management and filtering of large numbers of diverse genomic sequences for accurate analysis and inference on evolutionary processes of genomic and functional change. We developed Evolutionary Genomics and Biodiversity (EGenBio; ) to begin to address this. DESCRIPTION. 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. CONCLUSION. EGenBio was designed to serve as a platform for tools and resources to ease combined analysis in evolution, genomics, and biodiversity. en_US
dc.description.sponsorship National Institutes of Health (R22/R33 Innovation and Development Grant); National Science Foundation (CBM[2]/EPSCOR); State of Louisiana (Biological Compuational and Visualization Center, Governor's Biotechnology Initiative, startup funds) en_US
dc.language.iso en en_US
dc.publisher BioMed Central en_US
dc.rights Copyright 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. en_US
dc.rights.uri http://creativecommons.org/licenses/by/2.0 en_US
dc.title EGenBio: A Data Management System for Evolutionary Genomics and Biodiversity en_US
dc.type article en_US
dc.identifier.doi 10.1186/1471-2105-7-S2-S7 en_US
dc.identifier.pubmedid 17118150 en_US
dc.identifier.pmcid 1683573 en_US

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