DNA reference alignment benchmarks based on tertiary structure of encoded proteins.
BACKGROUND
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 3545 alignments, comprising of 68 581 sequences. Two versions of the database are available: mdsa_100s and mdsa_all. The mdsa_100s version contains the alignments of the data sets 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 data sets. The first such case study is included in the Supplementary Material.
Carroll
Hyrum
H
Computer Science Department, Brigham Young University, Provo, Utah 84602, USA. hyrumdc@gmail.com
Beckstead
Wesley
W
O'Connor
Timothy
T
Ebbert
Mark
M
Clement
Mark
M
Snell
Quinn
Q
McClellan
David
D
D019985:Benchmarking / Q000379:methods; D004247:DNA / Q000235:genetics*; D005815:Genetic Code / Q000235:genetics*; D017434:Protein Structure, Tertiary / Q000235:genetics*; D011506:Proteins / Q000737:chemistry / Q000235:genetics*; D012016:Reference Values; D016415:Sequence Alignment / Q000379:methods* / Q000592:standards*; D017422:Sequence Analysis, DNA / Q000379:methods* / Q000592:standards; D014481:United States
D011506:Proteins; D004247:DNA