How Well Does the HoT Score Reflect Sequence Alignment Accuracy? Export

@article{citeulike:3006093, abstract = {Multiple sequence alignment is an essential tool in many areas of biological research, and the accuracy of an alignment can strongly affect the accuracy of a downstream application such as phylogenetic analysis, identification of functional motifs, or polymerase chain reaction primer design. The heads or tails (HoT) method (Landan G, Graur D. 2007. Heads or tails: a simple reliability check for multiple sequence alignments. Mol Biol Evol. 24:1380-1383.) assesses the consistency of an alignment by comparing the alignment of a set of sequences with the alignment of the same set of sequences written in reverse order. This study shows that HoT scores and the alignment accuracies are positively correlated, so alignments with higher HoT scores are preferable. However, HoT scores are overestimates of alignment accuracy in general, with the extent of overestimation depending on the method used for multiple sequence alignment. 10.1093/molbev/msn103}, author = {Hall, Barry G.}, citeulike-article-id = {3006093}, citeulike-linkout-0 = {http://dx.doi.org/10.1093/molbev/msn103}, citeulike-linkout-1 = {http://mbe.oxfordjournals.org/content/25/8/1576.abstract}, citeulike-linkout-2 = {http://mbe.oxfordjournals.org/content/25/8/1576.full.pdf}, citeulike-linkout-3 = {http://mbe.oxfordjournals.org/cgi/content/abstract/25/8/1576}, citeulike-linkout-4 = {http://view.ncbi.nlm.nih.gov/pubmed/18458029}, citeulike-linkout-5 = {http://www.hubmed.org/display.cgi?uids=18458029}, day = {1}, doi = {10.1093/molbev/msn103}, journal = {Mol Biol Evol}, keywords = {2008, accuracy, alignment, hot, jctalk, multiple, sequence, testing}, month = {August}, number = {8}, pages = {1576--1580}, posted-at = {2008-11-25 15:47:13}, priority = {2}, title = {How Well Does the HoT Score Reflect Sequence Alignment Accuracy?}, url = {http://dx.doi.org/10.1093/molbev/msn103}, volume = {25}, year = {2008} }

TY - JOUR ID - citeulike:3006093 L3 - citeulike-article-id:3006093 N2 - Multiple sequence alignment is an essential tool in many areas of biological research, and the accuracy of an alignment can strongly affect the accuracy of a downstream application such as phylogenetic analysis, identification of functional motifs, or polymerase chain reaction primer design. The heads or tails (HoT) method (Landan G, Graur D. 2007. Heads or tails: a simple reliability check for multiple sequence alignments. Mol Biol Evol. 24:1380-1383.) assesses the consistency of an alignment by comparing the alignment of a set of sequences with the alignment of the same set of sequences written in reverse order. This study shows that HoT scores and the alignment accuracies are positively correlated, so alignments with higher HoT scores are preferable. However, HoT scores are overestimates of alignment accuracy in general, with the extent of overestimation depending on the method used for multiple sequence alignment. 10.1093/molbev/msn103 IS - 8 JF - Mol Biol Evol EP - 1580 TI - How Well Does the HoT Score Reflect Sequence Alignment Accuracy? VL - 25 SP - 1576 KW - 2008 KW - accuracy KW - alignment KW - hot KW - jctalk KW - multiple KW - sequence KW - testing AU - Hall, Barry PY - 2008/08/01/ UR - http://dx.doi.org/10.1093/molbev/msn103 ER -