Protein motif prediction by grammatical inference

Authors:
Piedachu Peris;Damián López;Marcelino Campos;José M. Sempere
Affiliations:
Departamento de Sistemas Informáticos y Computación., Universidad Politécnica de Valencia., Valencia, SPAIN;Departamento de Sistemas Informáticos y Computación., Universidad Politécnica de Valencia., Valencia, SPAIN;Departamento de Sistemas Informáticos y Computación., Universidad Politécnica de Valencia., Valencia, SPAIN;Departamento de Sistemas Informáticos y Computación., Universidad Politécnica de Valencia., Valencia, SPAIN
Venue:
ICGI'06 Proceedings of the 8th international conference on Grammatical Inference: algorithms and applications
Year:
2006

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Abstract

The rapid growth of protein sequence databases is exceeding the capacity of biochemically and structurally characterizing new proteins. Therefore, it is very important the development of tools to locate, within protein sequences, those subsequences with an associated function or specific feature. In our work, we propose a method to predict one of those functional motifs (coiled coil), related with protein interaction. Our approach uses even linear languages inference to obtain a transductor which will be used to label unknown sequences. The experiments carried out show that our method outperforms the results of previous approaches.