Therefore, there are eight possible combinations of specificity for alignment A, alignment B or the consensus (Fig. 1B).
The use of PE read alignments in this step is also important because the additional sequence information, provided by the second read in a PE, increases the specificity of the alignment process compared with single-end reads, and thus reduces the number of false read placements.
However, the preferred search programs and parameters that will optimise the sensitivity and specificity of the alignments between the sequence reads and the framework genome(s) are not necessarily obvious.
Next, we purified the mutant variant of PKD1 predicted to perturb the determinant of specificity in alignment position 494 that we named αD1, given its location on the first residue of α helix D of the kinase domain.
Within each genotype, this region could be aligned unambiguously with a high degree of specificity, but alignment between genotypes was problematic.
Most of techniques dealing with the stated problem reduce the problem of specificity prediction to the identification of alignment positions that may be important for protein specificity.
The specificity of ClinSeK short read alignment highly depends on the balance of its alignment sensitivity against the sensitivity to paralogous sites.
Due to the similarity in sequence between the M. truncatula SERK genes, each primer was checked for specificity against an alignment of the other M. truncatula SERK genes.
Motifs of interest were selected by applying a set of filters: specificity score [ 77], quality of alignment (AlignACE MAP score) [ 97], palindromicity [ 77], and conservation.
It makes use of the alignment specificity of BLASTZ and the sensitivity of DIALIGN.
Hence, Multiple Sequence Alignment methods need to adjust the underlying evolutionary hypothesis and the operators used as in the work published incorporating neighbouring base thermodynamic information to align the binding sites searching for the lowest thermodynamic alignment conserving specificity of the binding site, EDNA.
