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Prediction of Protein Function Improving Sequence Remote Alignment Search by a Fuzzy Logic Algorithm

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Abstract

The functional annotation of the new protein sequences represents a major drawback for genomic science. The best way to suggest the function of a protein from its sequence is by finding a related one for which biological information is available. Current alignment algorithms display a list of protein sequence stretches presenting significant similarity to different protein targets, ordered by their respective mathematical scores. However, statistical and biological significance do not always coincide, therefore, the rearrangement of the program output according to more biological characteristics than the mathematical scoring would help functional annotation. A new method that predicts the putative function for the protein integrating the results from the PSI-BLAST program and a fuzzy logic algorithm is described. Several protein sequence characteristics have been checked in their ability to rearrange a PSI-BLAST profile according more to their biological functions. Four of them: amino acid content, matched segment length and hydropathic and flexibility profiles positively contributed, upon being integrated by a fuzzy logic algorithm into a program, BYPASS, to the accurate prediction of the function of a protein from its sequence.

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Acknowledgements

This research was supported by Grant BFU 2004-06377 and BIO 2007-67904-C02-01 from the MCYT (Ministerio de Ciencia y Tecnologia, Spain) and by the Centre de Referència de R+D de Biotecnologia de la Generalitat de Catalunya. AH is a fellowship recipient from the Generalitat de Catalunya.

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Authors and Affiliations

  1. Institut de Biotecnologia i Biomedicina (IBB) and Departament de Bioquímica i Biologia Molecular de la, Universitat Autònoma de Barcelona (UAB), Bellaterra, Barcelona, 08193, Spain

    Antonio Gómez, Juan Cedano, Jordi Espadaler, Antonio Hermoso, Jaume Piñol & Enrique Querol

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  1. Antonio Gómez
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  2. Juan Cedano
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  3. Jordi Espadaler
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  4. Antonio Hermoso
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  5. Jaume Piñol
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  6. Enrique Querol
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Correspondence to Enrique Querol.

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Antonio Gómez and Juan Cedano contributed equally to this work.

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Gómez, A., Cedano, J., Espadaler, J. et al. Prediction of Protein Function Improving Sequence Remote Alignment Search by a Fuzzy Logic Algorithm. Protein J 27, 130–139 (2008). https://doi.org/10.1007/s10930-007-9116-x

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