Predicting functional residues of protein sequence alignments as a feature selection task

Haddow, Chris, Perry, Justin, Durrant, Marcus and Faith, Joe (2011) Predicting functional residues of protein sequence alignments as a feature selection task. International Journal of Data Mining in Bioinformatics, 5 (6). pp. 691-705. ISSN 1748-5673

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Determining which residues within a multiple alignment of protein sequences are most responsible for protein function is a difficult and important task in bioinformatics. Here, we show that this task is an application of the standard Feature Selection (FS) problem. We show the comparison of standard FS techniques with more specialised algorithms on a range of data sets backed by experimental evidence, and find that some standard algorithms perform as well as specialised ones. We also discuss how considering the discriminating power of combinations of residue positions, rather than the power of each position individually, has the potential to improve the performance of such algorithms.

Item Type: Article
Uncontrolled Keywords: feature selection, protein structure, functional residue prediction, targeted projection pursuit, information gain
Subjects: F100 Chemistry
F400 Forensic and Archaeological Science
G500 Information Systems
Department: Faculties > Health and Life Sciences > Applied Sciences
Faculties > Engineering and Environment > Mathematics, Physics and Electrical Engineering
Depositing User: Ellen Cole
Date Deposited: 16 Dec 2011 10:54
Last Modified: 24 Oct 2017 11:26

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