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Bioinformatics Advance Access originally published online on February 19, 2004
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Bioinformatics 20(8) © Oxford University Press 2004; all rights reserved.

Prediction of Saccharomyces cerevisiae protein functional class from functional domain composition

Yu-Dong Cai and Andrew J. Doig *

Department of Biomolecular Sciences, UMIST, P.O. Box 88, Manchester M60 1QD, UK

Received on April 13, 2003; revised on August 13, 2003; accepted on October 23, 2003
Advance Access Publication February 19, 2004

Motivation: A key goal of genomics is to assign function to genes, especially for orphan sequences.

Results: We compared the clustered functional domains in the SBASE database to each protein sequence using BLASTP. This representation for a protein is a vector, where each of the non-zero entries in the vector indicates a significant match between the sequence of interest and the SBASE domain. The machine learning methods nearest neighbour algorithm (NNA) and support vector machines are used for predicting protein functional classes from this information. We find that the best results are found using the SBASE-A database and the NNA, namely 72% accuracy for 79% coverage. We tested an assigning function based on searching for InterPro sequence motifs and by taking the most significant BLAST match within the dataset. We applied the functional domain composition method to predict the functional class of 2018 currently unclassified yeast open reading frames.

Availability: A program for the prediction method, that uses NNA called Functional Class Prediction based on Functional Domains (FCPFD) is available and can be obtained by contacting Y.D.Cai at y.cai{at}umist.ac.uk

Contact: Andrew.Doig{at}umist.ac.uk

* To whom correspondence should be addressed.


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