Sentence examples for benchmark alignment from inspiring English sources
The first exhaustive protein alignment benchmark [ 10] used the so called BAliBASE (Benchmark Alignment dataBASE) [ 11].
The predicted alignment was compared to the benchmark alignment in BAliBASE 3.0 to compute the sensitivity and the positive predictive value, where TP is the number of correctly aligned symbol pairs, FP is the number of incorrectly aligned pairs, and FN is the number of symbol pairs that are aligned in the benchmark alignment but not aligned in the predicted alignment.
We compared both accuracy and cost of nine popular MSA programs, namely CLUSTALW, CLUSTAL OMEGA, DIALIGN-TX, MAFFT, MUSCLE, POA, Probalign, Probcons and T-Coffee, against the benchmark alignment dataset BAliBASE and discuss the relevance of some implementations embedded in each program's algorithm.
The resulting benchmark alignments reflect some of the problems specific to aligning large sets of complex protein sequences.
Details of the benchmark alignments are provided in the Methods section.
As test data for genomic sequence comparison, we used a set of 27 primate mitochondrial genomes that have been previously used by Haubold et al. (2009) to benchmark alignment-free methods.
To compare the output of different programs to the respective benchmark alignments, we used C. Notredame's program aln_compare [ 32].
A set of benchmark alignments is selected as described in the Methods section, in order to estimate the number of long-range (or non trivial) contacts of amino acids, with respect to the general topohydrophobic index deduced from the multiple sequence alignment and to the associated secondary structure.
The BRAliBase (Benchmark RNA Alignment dataBase) dataset used in the first comprehensive RNA alignment benchmark published so far [ 22] was constructed using alignments from release 5.0 of the Rfam database [ 23], a large collection of hand-curated multiple RNA sequence alignments.
For benchmarking of alignment quality we used Pfam version 22.0 [ 15], BAliBase Version 3 [ 22] and HOMSTRAD, downloaded on 2009-06-09 [ 21].
The following sequence sets were used in our study: For eukaryotic DNA comparison, we used a set of 27 primate mitochondrial genomes that were previously used by Haubold et al. (2009) as benchmark for alignment-free methods.
