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OXBench: a benchmark for evaluation of protein multiple sequence alignment accuracy.

DIR@IMTECH: CSIR-Institute of Microbial Technology

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Title OXBench: a benchmark for evaluation of protein multiple sequence alignment accuracy.
 
Creator Raghava, G.P.S.
Searle, Stephen M J
Audley, Patrick C
Barber, Jonathan D
Barton, Geoffrey J
 
Subject QR Microbiology
 
Description 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.
 
Publisher Biomedcentral
 
Date 2003-10-10
 
Type Article
PeerReviewed
 
Format application/pdf
 
Identifier http://crdd.osdd.net/open/93/1/raghava2003.1.pdf
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
 
Relation http://www.biomedcentral.com/content/pdf/1471-2105-4-47.pdf
http://crdd.osdd.net/open/93/