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Wiley InterScience | ||||||||||||||||
  FEBS JournalVolume 272 Issue 20, Pages 5119 - 5128 Published Online: 7 Oct 2005 Journal compilation © 2010 Federation of European Biochemical Societies Published on behalf of the Federation of European Biochemical Societies
Abstract | References | Full Text: HTML, PDF (Size: 453K) | Related Articles | Citation Tracking  MINIREVIEW Identifying remote protein homologs by network propagation Copyright 2005 FEBS KEYWORDS network diffusion • protein homology • protein networks • sequence comparison ABSTRACTPerhaps the most widely used applications of bioinformatics are tools such as psi-blast for searching sequence databases. We describe a recently developed protein database search algorithm called rankprop. rankprop relies upon a precomputed network of pairwise protein similarities. The algorithm performs a diffusion operation from a specified query protein across the protein similarity network. The resulting activation scores, assigned to each database protein, encode information about the global structure of the protein similarity network. This type of algorithm has a rich history in associationist psychology, artificial intelligence and web search. We describe the rankprop algorithm and its relatives, and we provide evidence that the algorithm successfully improves upon the rankings produced by psi-blast. (Received 25 May 2005, revised 19 August 2005, accepted 30 August 2005) | 
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