TAILIEUCHUNG - Báo cáo khoa học: Identifying remote protein homologs by network propagation

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 calledrankprop. 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. | ềFEBS Journal MINIREVIEW Identifying remote protein homologs by network propagation William S. Noble1 Rui Kuang2 Christina Leslie3 and Jason Weston4 1 Department of Genome Sciences Department of Computer Science and Engineering University of Washington Seattle WA USA 2 Department of Computer Science Columbia University New York NY USA 3 Center for ComputationalLearning Systems Columbia University New York NY USA 4 NEC Laboratories America Princeton NJ USA Keywords network diffusion protein homology protein networks sequence comparison Correspondence W. S. Noble Department of Genome Sciences Department of Computer Science and Engineering University of Washington Seattle WA USA Fax 1 206 685 7301 Tel 1 206 543 8930 E-mail noble@ Received 25 May 2005 revised 19 August 2005 accepted 30 August 2005 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. doi Introduction Networks abound in the scientific literature these days. Some of these networks gene regulatory networks metabolic networks protein-protein interaction networks represent real biological phenomena. Other networks are useful abstractions that allow for formal reasoning to occur. Recently we described a .

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