%A G.P.S. Raghava
%A Stephen M J Searle
%A Patrick C Audley
%A Jonathan D Barber
%A Geoffrey J Barton
%O OPEN ACCESS
%J BMC bioinformatics
%T OXBench: a benchmark for evaluation of protein multiple sequence alignment accuracy.
%X 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.
%P 47
%V 4
%D 2003
%I Biomedcentral
%L open93