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An assessment of feature relevance in predicting protein function from sequence

Al-Shahib, A; He, C; Tan, AC; Girolami, M; Gilbert, D; (2004) An assessment of feature relevance in predicting protein function from sequence. In: Yang, ZR and Everson, R and Yin, H, (eds.) INTELLIGENT DATA ENGINEERING AND AUTOMATED LEARNING IDEAL 2004, PROCEEDINGS. (pp. 52 - 57). SPRINGER-VERLAG BERLIN

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Abstract

Improving the performance of protein function prediction is the ultimate goal for a bioinformatician 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.

Type:Proceedings paper
Title:An assessment of feature relevance in predicting protein function from sequence
Event:5th International Conference on Intelligent Data Engineering and Automated Learning (IDEAL 2004)
Location:Execter, ENGLAND
Dates:2004-08-25 - 2004-08-27
ISBN:3-540-22881-0
UCL classification:UCL > School of BEAMS > Faculty of Maths and Physical Sciences > Statistical Science

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