Identifying remote protein homologs by network propagation

William S. Noble, Rui Kuang, Christina Leslie, Jason Weston

Research output: Contribution to journalShort surveypeer-review

22 Scopus citations

Abstract

Perhaps 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.

Original languageEnglish (US)
Pages (from-to)5119-5128
Number of pages10
JournalFEBS Journal
Volume272
Issue number20
DOIs
StatePublished - Oct 1 2005

Keywords

  • Network diffusion
  • Protein homology
  • Protein networks
  • Sequence comparison

Fingerprint

Dive into the research topics of 'Identifying remote protein homologs by network propagation'. Together they form a unique fingerprint.

Cite this