swMATH ID: 22988
Software Authors: Raghava GPS, Searle SMJ, Audley PC, Barber JD, Barton GJ
Description: OXBench: a benchmark for evaluation of protein multiple sequence alignment accuracy. BACKGROUND: The alignment of two or more protein sequences provides a powerful guide in the prediction of the protein structure and in identifying key functional residues, however, the utility of any prediction is completely dependent on the accuracy of the alignment. In this paper we describe a suite of reference alignments derived from the comparison of protein three-dimensional structures together with evaluation measures and software that allow automatically generated alignments to be benchmarked. We test the OXBench benchmark suite on alignments generated by the AMPS multiple alignment method, then apply the suite to compare eight different multiple alignment algorithms. The benchmark shows the current state-of-the art for alignment accuracy and provides a baseline against which new alignment algorithms may be judged. RESULTS: The simple hierarchical multiple alignment algorithm, AMPS, performed as well as or better than more modern methods such as CLUSTALW once the PAM250 pair-score matrix was replaced by a BLOSUM series matrix. AMPS gave an accuracy in Structurally Conserved Regions (SCRs) of 89.9
Homepage: https://www.ncbi.nlm.nih.gov/pubmed/14552658
Related Software: ClustalW; SABmark; MUSCLE; MrBayes; Mauve; Kalign; HMMER; Balibase; T-coffee; ProbCons; PAUP*; iGTP; ProtTest 3; Probalign; SATe; PartTree; Mugsy; LAGAN; BIONJ; RAxML
Cited in: 5 Documents

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Oxbench: A benchmark for evaluation of protein multiple sequence alignment accuracy
Raghava, Gps; Searle, Stephen Mj.; Audley, Patrick C.; Barber, Jonathan D.; Barton, Geoffrey J.

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