Fold recognition by combining profile-profile alignment and support vector machine.
Bioinformatics
; 21(11): 2667-73, 2005 Jun 01.
Article
en En
| MEDLINE
| ID: mdl-15769835
ABSTRACT
MOTIVATION Currently, the most accurate fold-recognition method is to perform profile-profile alignments and estimate the statistical significances of those alignments by calculating Z-score or E-value. Although this scheme is reliable in recognizing relatively close homologs related at the family level, it has difficulty in finding the remote homologs that are related at the superfamily or fold level. RESULTS:
In this paper, we present an alternative method to estimate the significance of the alignments. The alignment between a query protein and a template of length n in the fold library is transformed into a feature vector of length n + 1, which is then evaluated by support vector machine (SVM). The output from SVM is converted to a posterior probability that a query sequence is related to a template, given SVM output. Results show that a new method shows significantly better performance than PSI-BLAST and profile-profile alignment with Z-score scheme. While PSI-BLAST and Z-score scheme detect 16 and 20% of superfamily-related proteins, respectively, at 90% specificity, a new method detects 46% of these proteins, resulting in more than 2-fold increase in sensitivity. More significantly, at the fold level, a new method can detect 14% of remotely related proteins at 90% specificity, a remarkable result considering the fact that the other methods can detect almost none at the same level of specificity.
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Colección:
01-internacional
Base de datos:
MEDLINE
Asunto principal:
Algoritmos
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Reconocimiento de Normas Patrones Automatizadas
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Inteligencia Artificial
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Proteínas
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Alineación de Secuencia
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Análisis de Secuencia de Proteína
Tipo de estudio:
Evaluation_studies
Idioma:
En
Revista:
Bioinformatics
Asunto de la revista:
INFORMATICA MEDICA
Año:
2005
Tipo del documento:
Article
Pais de publicación:
ENGLAND
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ESCOCIA
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GB
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GREAT BRITAIN
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INGLATERRA
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REINO UNIDO
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SCOTLAND
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UK
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UNITED KINGDOM