RANKPROP: a web server for protein remote homology detection Export

@article{citeulike:3871047, abstract = {Summary: We present a large-scale implementation of the RANKPROP protein homology ranking algorithm in the form of an openly accessible web server. We use the NRDB40 PSI-BLAST all-versus-all protein similarity network of 1.1 million proteins to construct the graph for the RANKPROP algorithm, whereas previously, results were only reported for a database of 108 000 proteins. We also describe two algorithmic improvements to the original algorithm, including propagation from multiple homologs of the query and better normalization of ranking scores, that lead to higher accuracy and to scores with a probabilistic interpretation. Availability: The RANKPROP web server and source code are available at http://rankprop.gs.washington.edu Contact: iain@nec-labs.com; noble@gs.washington.edu 10.1093/bioinformatics/btn567}, author = {Melvin, Iain and Weston, Jason and Leslie, Christina and Noble, William S.}, citeulike-article-id = {3871047}, citeulike-linkout-0 = {http://dx.doi.org/10.1093/bioinformatics/btn567}, citeulike-linkout-1 = {http://bioinformatics.oxfordjournals.org/cgi/content/abstract/25/1/121}, citeulike-linkout-2 = {http://view.ncbi.nlm.nih.gov/pubmed/18990723}, citeulike-linkout-3 = {http://www.hubmed.org/display.cgi?uids=18990723}, day = {1}, doi = {10.1093/bioinformatics/btn567}, journal = {Bioinformatics}, keywords = {networks, protein, similarity}, month = {January}, number = {1}, pages = {121--122}, posted-at = {2009-01-09 20:18:23}, priority = {4}, title = {RANKPROP: a web server for protein remote homology detection}, url = {http://dx.doi.org/10.1093/bioinformatics/btn567}, volume = {25}, year = {2009} }

TY - JOUR ID - citeulike:3871047 L3 - citeulike-article-id:3871047 N2 - Summary: We present a large-scale implementation of the RANKPROP protein homology ranking algorithm in the form of an openly accessible web server. We use the NRDB40 PSI-BLAST all-versus-all protein similarity network of 1.1 million proteins to construct the graph for the RANKPROP algorithm, whereas previously, results were only reported for a database of 108 000 proteins. We also describe two algorithmic improvements to the original algorithm, including propagation from multiple homologs of the query and better normalization of ranking scores, that lead to higher accuracy and to scores with a probabilistic interpretation. Availability: The RANKPROP web server and source code are available at http://rankprop.gs.washington.edu Contact: iain@nec-labs.com; noble@gs.washington.edu 10.1093/bioinformatics/btn567 IS - 1 JF - Bioinformatics EP - 122 TI - RANKPROP: a web server for protein remote homology detection VL - 25 SP - 121 KW - networks KW - protein KW - similarity AU - Melvin, Iain AU - Weston, Jason AU - Leslie, Christina AU - Noble, William PY - 2009/01/01/ UR - http://dx.doi.org/10.1093/bioinformatics/btn567 ER -