Analysis and comparison of benchmarks for multiple sequence alignment. Export

@article{Blackshields2006, abstract = {The most popular way of comparing the performance of multiple sequence alignment programs is to use empirical testing on sets of test sequences. Several such test sets now exist, each with potential strengths and weaknesses. We apply several different alignment packages to 6 benchmark datasets, and compare their relative performances. HOMSTRAD, a collection of alignments of homologous proteins, is regularly used as a benchmark for sequence alignment though it is not designed as such, and lacks annotation of reliable regions within the alignment. We introduce this annotation into HOMSTRAD using protein structural superposition. Results on each database show that method performance is dependent on the input sequences. Alignment benchmarks are regularly used in combination to measure performance across a spectrum of alignment problems. Through combining benchmarks, it is possible to detect whether a program has been over-optimised for a single dataset, or alignment problem type.}, author = {Blackshields, G. and Wallace, I. M. and Larkin, M. and Higgins, D. G.}, citeulike-article-id = {4623827}, citeulike-linkout-0 = {http://view.ncbi.nlm.nih.gov/pubmed/16922695}, citeulike-linkout-1 = {http://www.hubmed.org/display.cgi?uids=16922695}, issn = {1386-6338}, journal = {In silico biology}, keywords = {alignment, evaluation, method}, number = {4}, pages = {321--339}, posted-at = {2009-05-24 21:41:46}, priority = {0}, title = {Analysis and comparison of benchmarks for multiple sequence alignment.}, url = {http://view.ncbi.nlm.nih.gov/pubmed/16922695}, volume = {6}, year = {2006} }

TY - JOUR ID - Blackshields2006 L3 - citeulike-article-id:4623827 N2 - The most popular way of comparing the performance of multiple sequence alignment programs is to use empirical testing on sets of test sequences. Several such test sets now exist, each with potential strengths and weaknesses. We apply several different alignment packages to 6 benchmark datasets, and compare their relative performances. HOMSTRAD, a collection of alignments of homologous proteins, is regularly used as a benchmark for sequence alignment though it is not designed as such, and lacks annotation of reliable regions within the alignment. We introduce this annotation into HOMSTRAD using protein structural superposition. Results on each database show that method performance is dependent on the input sequences. Alignment benchmarks are regularly used in combination to measure performance across a spectrum of alignment problems. Through combining benchmarks, it is possible to detect whether a program has been over-optimised for a single dataset, or alignment problem type. IS - 4 JF - In silico biology SN - 1386-6338 EP - 339 TI - Analysis and comparison of benchmarks for multiple sequence alignment. VL - 6 SP - 321 KW - alignment KW - evaluation KW - method AU - Blackshields, G AU - Wallace, IM AU - Larkin, M AU - Higgins, DG PY - 2006/// UR - http://view.ncbi.nlm.nih.gov/pubmed/16922695 ER -