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MBE Advance Access published online on May 4, 2008
Molecular Biology and Evolution, doi:10.1093/molbev/msn103
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© The Author 2008. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. All rights reserved. For permissions, please e-mail: journals.permissions@oxfordjournals.org

Research Article

How well does the HoT score reflect sequence alignment accuracy?

Barry G. Hall

Barry G. Hall, Bellingham Research Institute, Bellingham, WA 98229 USA, drbh{at}mail.rochester.edu, barryhall{at}zeninternet.com

Received for publication March 14, 2008. Revision received April 20, 2008. Accepted for publication April 27, 2008.

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 PCR primer design. The HoT (Heads or Tails) method (Landan and Graur 2007) 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.

Key Words: sequence alignment accuracy • HoT consistency • alignment methods


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