RANKPROP: A web server for protein remote homology detection Journal Article
| Authors: | Melvin, I.; Weston, J.; Leslie, C.; Noble, W. S. |
| Article Title: | RANKPROP: A web server for protein remote homology detection |
| Abstract: | 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. © The Author 2008. Published by Oxford University Press. All rights reserved. |
| Keywords: | controlled study; accuracy; computational biology; internet; algorithms; databases, protein; access to information; amino acid sequence; algorithm; probability; data analysis; scoring system; sequence homology; bioinformatics; protein database; protein determination; roc curve; computer network; structural homology, protein |
| Journal Title: | Bioinformatics |
| Volume: | 25 |
| Issue: | 1 |
| ISSN: | 1367-4803 |
| Publisher: | Oxford University Press |
| Date Published: | 2009-01-01 |
| Start Page: | 121 |
| End Page: | 122 |
| Language: | English |
| DOI: | 10.1093/bioinformatics/btn567 |
| PUBMED: | 18990723 |
| PROVIDER: | scopus |
| PMCID: | PMC2638939 |
| DOI/URL: | |
| Notes: | --- - "Cited By (since 1996): 1" - "Export Date: 30 November 2010" - "CODEN: BOINF" - "Source: Scopus" |
