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ConFunc--functional annotation in the twilight zone

Wass, Mark N., Sternberg, Michael J.E. (2008) ConFunc--functional annotation in the twilight zone. Bioinformatics, 24 (6). pp. 798-806. ISSN 1367-4803. (doi:10.1093/bioinformatics/btn037) (The full text of this publication is not currently available from this repository. You may be able to access a copy if URLs are provided)

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Official URL
http://dx.doi.org/10.1093/bioinformatics/btn037

Abstract

Motivation: The success of genome sequencing has resulted in many protein sequences without functional annotation. We present ConFunc, an automated Gene Ontology (GO)-based protein function prediction approach, which uses conserved residues to generate sequence profiles to infer function. ConFunc split sets of sequences identified by PSI-BLAST into sub-alignments according to their GO annotations. Conserved residues are identified for each GO term sub-alignment for which a position specific scoring matrix is generated. This combination of steps produces a set of feature (GO annotation) derived profiles from which protein function is predicted. Results: We assess the ability of ConFunc, BLAST and PSI-BLAST to predict protein function in the twilight zone of sequence similarity. ConFunc significantly outperforms BLAST & PSI-BLAST obtaining levels of recall and precision that are not obtained by either method and maximum precision 24% greater than BLAST. Further for a large test set of sequences with homologues of low sequence identity, at high levels of presicision, ConFunc obtains recall six times greater than BLAST. These results demonstrate the potential for ConFunc to form part of an automated genomics annotation pipeline.

Item Type: Article
DOI/Identification number: 10.1093/bioinformatics/btn037
Subjects: Q Science
Divisions: Faculties > Sciences > School of Biosciences
Depositing User: Mark Wass
Date Deposited: 09 Oct 2012 11:11 UTC
Last Modified: 29 May 2019 09:31 UTC
Resource URI: https://kar.kent.ac.uk/id/eprint/31434 (The current URI for this page, for reference purposes)
Wass, Mark N.: https://orcid.org/0000-0001-5428-6479
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