An assessment of feature relevance in predicting protein function from sequence

Ali Al-Shahib, Chao He, Aik-Choon Tan, Mark Girolami, David Gilbert

Research output: Contribution to journalArticle

1 Citation (Scopus)


Improving the performance of protein function prediction is the ultimate goal for a bioinforraatician working in functional genomics. The classical prediction approach is to employ pairwise sequence alignments. However this method often faces difficulties when no statistically significant homologous sequences are identified. An alternative way is to predict protein function from sequence-derived features using machine learning. In this case the choice of possible features which can be derived from the sequence is of vital importance to ensure adequate discrimination to predict function. In this paper we have shown that carefully assessing the discriminative value of derived features by performing feature selection improves the performance of the prediction classifiers by eliminating irrelevant and redundant features. The subset selected from available features has also shown to be biologically meaningful as they correspond to features that have commonly been employed to assess biological function.

Original languageEnglish
Pages (from-to)52-57
Number of pages6
JournalLecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)
Publication statusPublished - 2004 Dec 1
Externally publishedYes

ASJC Scopus subject areas

  • Computer Science(all)
  • Biochemistry, Genetics and Molecular Biology(all)
  • Theoretical Computer Science

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