The Princeton Protein Orthology Database (P-POD): a comparative genomics analysis tool for biologists. Export

@article{citeulike:1969816, abstract = {Many biological databases that provide comparative genomics information and tools are now available on the internet. While certainly quite useful, to our knowledge none of the existing databases combine results from multiple comparative genomics methods with manually curated information from the literature. Here we describe the Princeton Protein Orthology Database (P-POD, http://ortholog.princeton.edu), a user-friendly database system that allows users to find and visualize the phylogenetic relationships among predicted orthologs (based on the OrthoMCL method) to a query gene from any of eight eukaryotic organisms, and to see the orthologs in a wider evolutionary context (based on the Jaccard clustering method). In addition to the phylogenetic information, the database contains experimental results manually collected from the literature that can be compared to the computational analyses, as well as links to relevant human disease and gene information via the OMIM, model organism, and sequence databases. Our aim is for the P-POD resource to be extremely useful to typical experimental biologists wanting to learn more about the evolutionary context of their favorite genes. P-POD is based on the commonly used Generic Model Organism Database (GMOD) schema and can be downloaded in its entirety for installation on one's own system. Thus, bioinformaticians and software developers may also find P-POD useful because they can use the P-POD database infrastructure when developing their own comparative genomics resources and database tools.}, address = {Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, New Jersey, United States of America.}, author = {Heinicke, S. and Livstone, M. S. and Lu, C. and Oughtred, R. and Kang, F. and Angiuoli, S. V. and White, O. and Botstein, D. and Dolinski, K.}, citeulike-article-id = {1969816}, citeulike-linkout-0 = {http://dx.doi.org/10.1371/journal.pone.0000766}, citeulike-linkout-1 = {http://view.ncbi.nlm.nih.gov/pubmed/17712414}, citeulike-linkout-2 = {http://www.hubmed.org/display.cgi?uids=17712414}, doi = {10.1371/journal.pone.0000766}, issn = {1932-6203}, journal = {PLoS ONE}, keywords = {browser, chado, gmod, ortholog, proteome}, number = {1}, posted-at = {2008-11-12 12:34:36}, priority = {2}, title = {The Princeton Protein Orthology Database (P-POD): a comparative genomics analysis tool for biologists.}, url = {http://dx.doi.org/10.1371/journal.pone.0000766}, volume = {2}, year = {2007} }

TY - JOUR ID - citeulike:1969816 L3 - citeulike-article-id:1969816 N2 - Many biological databases that provide comparative genomics information and tools are now available on the internet. While certainly quite useful, to our knowledge none of the existing databases combine results from multiple comparative genomics methods with manually curated information from the literature. Here we describe the Princeton Protein Orthology Database (P-POD, http://ortholog.princeton.edu), a user-friendly database system that allows users to find and visualize the phylogenetic relationships among predicted orthologs (based on the OrthoMCL method) to a query gene from any of eight eukaryotic organisms, and to see the orthologs in a wider evolutionary context (based on the Jaccard clustering method). In addition to the phylogenetic information, the database contains experimental results manually collected from the literature that can be compared to the computational analyses, as well as links to relevant human disease and gene information via the OMIM, model organism, and sequence databases. Our aim is for the P-POD resource to be extremely useful to typical experimental biologists wanting to learn more about the evolutionary context of their favorite genes. P-POD is based on the commonly used Generic Model Organism Database (GMOD) schema and can be downloaded in its entirety for installation on one's own system. Thus, bioinformaticians and software developers may also find P-POD useful because they can use the P-POD database infrastructure when developing their own comparative genomics resources and database tools. IS - 1 JF - PLoS ONE SN - 1932-6203 AD - Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, New Jersey, United States of America. TI - The Princeton Protein Orthology Database (P-POD): a comparative genomics analysis tool for biologists. VL - 2 KW - browser KW - chado KW - gmod KW - ortholog KW - proteome AU - Heinicke, S AU - Livstone, MS AU - Lu, C AU - Oughtred, R AU - Kang, F AU - Angiuoli, SV AU - White, O AU - Botstein, D AU - Dolinski, K PY - 2007/// UR - http://dx.doi.org/10.1371/journal.pone.0000766 ER -