Identifying remote protein homologs by network propagation.

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

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

Afiliación

Noble WS; Department of Genome Sciences Department of Computer Science and Engineering University of Washington Seattle, WA, USA. noble@gs.washington.edu

FEBS J ; 272(20): 5119-28, 2005 Oct.

Article en En | MEDLINE | ID: mdl-16218946

RESUMEN

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.

Asunto(s)

Algoritmos; Biología Computacional/métodos; Alineación de Secuencia/métodos; Proteínas Bacterianas/genética; Bases de Datos de Proteínas; Internet; Fotorreceptores Microbianos/genética; Estructura Terciaria de Proteína/genética; Proteínas/genética; Curva ROC

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Colección: 01-internacional Base de datos: MEDLINE Asunto principal: Algoritmos / Alineación de Secuencia / Biología Computacional Tipo de estudio: Prognostic_studies Idioma: En Revista: FEBS J Asunto de la revista: BIOQUIMICA Año: 2005 Tipo del documento: Article País de afiliación: Estados Unidos Pais de publicación: Reino Unido

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