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Bioinformatics Advance Access published online on August 8, 2007
Bioinformatics, doi:10.1093/bioinformatics/btm389
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© The Author (2007). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org

DNA Reference Alignment Benchmarks Based on Tertiary Structure of Encoded Proteins

Hyrum Carroll a,*, Wesley Beckstead b, Timothy O'Connor b, Mark Ebbert a,b, Mark Clement a, Quinn Snell a and David McClellan b

aComputer Science Department, b Biology Department, Brigham Young University Provo, Utah 84602, USA

*To whom correspondence should be addressed. Hyrum Carroll, E-mail: hdc{at}cs.byu.edu


  Abstract

Motivation: Multiple sequence alignments (MSAs) are at the heart of bioinformatics analysis. Recently, a number of multiple protein sequence alignment benchmarks (i.e., BAliBASE, OXBench, PREFAB and SMART) have been released to evaluate new and existing MSA applications. These databases have been well received by researchers and help to quantitatively evaluate MSA programs on protein sequences. Unfortunately, analogous DNA benchmarks are not available, making evaluation of MSA programs difficult for DNA sequences.

Results: This work presents the first known multiple DNA sequence alignment benchmarks that are 1) comprised of protein-coding portions of DNA 2) based on biological features such as the tertiary structure of encoded proteins. These reference DNA databases contain a total of 3,545 alignments, comprising of 68,581 sequences. Two versions of the database are available: mdsa_100s and mdsa_all. The mdsa100s version contains the alignments of the datasets that TBLASTN found 100% sequence identity for each sequence. The mdsa_all version includes all hits with an E-value score above the threshold of 0.001 A primary use of these databases is to benchmark the performance of MSA applications on DNA datasets. The first such case study is included in the supplementary material.

Availability: The databases, further details and the supplementary material are publicly available at http://csl.cs.byu.edu/mdsas/.

Contact: hdc{at}cs.byu.edu

Associate Editor: Prof. John Quackenbush

Received on April 7, 2007; revised on July 19, 2007; accepted on July 22, 2007

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