DNA reference alignment benchmarks based on tertiary structure of encoded proteins

Abstract

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.

Molecular phylogenetic assessment of host range in five Dermanyssus species

“…MAFFT with the L-INS-i option has shown to be the most accurate and consistent method for the alignment of sequences (Wilm et al 2006;Carroll et al 2007). The alignment of 558 bp from cytochrome oxidase I (mt-COI) was analysed under several optimality criteria: (1) Parsimony using PAUP* 4.0b10 (Swofford 2001) to build tree(s) with TBR branch swapping and 10,000 random additions saving all most parsimonious trees, (2) Bayesian inference using the computer program MrBayes v3.1.2 (Huelsenbeck and Ronquist 2001;Ronquist and Huelsenbeck 2003) with the GTR ?…”

Comparison of Data Partitioning Schema of Parallel Pairwise Alignment on Shared Memory System

“…This algorithm correctness is verified by aligning two sequences from BAliBASE DNA sequence alignment benchmark [18]. These sequences are Saccharomyces cereviseae GlyRS1 (SYG_YEAST) and Schizosaccharomyces pombe GlyRS (SYG_SCHPO).…”

Large-Scale Multiple Sequence Alignment and Phylogeny Estimation

“…The best known of these benchmark datasets is probably BAliBASE [94], but others are also used [95][96][97][98]. The choice of benchmarks and how they are used has a large impact on the result of the evaluation, and so has been discussed in several papers [24,78,[99][100][101].…”

“…The use of treelength optimization to find good trees (and/or alignments) is a matter of substantial controversy in phylogenetics [98,102,227,248,[258][259][260][261]. Most of the studies that have examined the accuracy of POY trees and alignments explored performance under simple gap penalties, and found that POY did not produce trees and alignments of comparable accuracy to maximum parsimony on the ClustalW alignment, denoted MP(Clustal) [259,262].…”