Melvin Iain, Weston Jason, Leslie Christina, Noble William Stafford
NEC Laboratories of America, Princeton, NJ, USA.
Bioinformatics. 2009 Jan 1;25(1):121-2. doi: 10.1093/bioinformatics/btn567. Epub 2008 Nov 6.
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 Rankprop web server and source code are available at http://rankprop.gs.washington.edu
我们以一个可公开访问的网络服务器的形式展示了Rankprop蛋白质同源性排序算法的大规模实现。我们使用包含110万个蛋白质的NRDB40 PSI-BLAST全对全蛋白质相似性网络来构建Rankprop算法的图，而此前仅针对108000个蛋白质的数据库报告了结果。我们还描述了对原始算法的两项算法改进，包括从查询的多个同源物进行传播以及对排序分数进行更好的归一化，这导致了更高的准确性和具有概率解释的分数。
Rankprop网络服务器和源代码可在http://rankprop.gs.washington.edu获得
