creators_name: Raghava, G.P.S.
creators_name: Searle, Stephen M J
creators_name: Audley, Patrick C
creators_name: Barber, Jonathan D
creators_name: Barton, Geoffrey J
type: article
datestamp: 2012-01-10 08:06:21
lastmod: 2012-01-10 08:06:21
metadata_visibility: show
title: OXBench: a benchmark for evaluation of protein multiple sequence alignment accuracy.
ispublished: pub
subjects: QR
full_text_status: public
note: OPEN ACCESS
abstract: The OXBench suite of reference alignments, evaluation software and results database provide a convenient method to assess progress in sequence alignment techniques. Evaluation measures that were dependent on comparison to a reference alignment were found to give good discrimination between methods. The STAMP Sc Score which is independent of a reference alignment also gave good discrimination. Application of OXBench in this paper shows that with the exception of T-COFFEE, the majority of the improvement in alignment accuracy seen since 1985 stems from improved pair-score matrices rather than algorithmic refinements. The maximum theoretical alignment accuracy obtained by pooling results over all methods was 94.5% with 52.5% accuracy for alignments in the 0-10 percentage identity range. This suggests that further improvements in accuracy will be possible in the future.
date: 2003-10-10
date_type: published
publication: BMC bioinformatics
volume: 4
publisher: Biomedcentral
pagerange: 47
refereed: TRUE
issn: 1471-2105
official_url: http://www.biomedcentral.com/content/pdf/1471-2105-4-47.pdf
related_url_url: http://www.compbio.dundee.ac.uk/
related_url_type: author
citation:   Raghava, G.P.S. and Searle, Stephen M J and Audley, Patrick C and Barber, Jonathan D and Barton, Geoffrey J  (2003) OXBench: a benchmark for evaluation of protein multiple sequence alignment accuracy.  BMC bioinformatics, 4.  p. 47.  ISSN 1471-2105     
document_url: http://crdd.osdd.net/open/93/1/raghava2003.1.pdf