Prediction of Saccharomyces cerevisiae protein functional class from functional domain composition

Yu Dong Cai, Andrew J. Doig

    Research output: Contribution to journalArticlepeer-review


    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. © Oxford University Press 2004; all rights reserved.
    Original languageEnglish
    Pages (from-to)1292-1300
    Number of pages8
    Issue number8
    Publication statusPublished - 22 May 2004


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