Authors' response: Mauve alignment generates an identity matrix file which calculates the identity score range between 0 and 1; 0 indicates no homologous nucleotides and 1 indicates that every homologous nucleotide was identical.
Final assembling of each aligned group was performed using profile alignment generating a final dataset of 6,244 sites.
Comparison by multiple sequence alignment generated a dendrogram, revealing the phylogenetic relationships of CrGSTs with other well-characterized GST classes.
Initially, the sequences were subjected to Clustal W multiple sequence alignment generating a consensus sequence (Figure 4A).
The multiple sequence alignment generated a matrix consisting of 44 taxonomic entities and 552 nucleotide sites, of which 490 were invariant, 25 variable but parsimony-uninformative, and 37 variable and parsimony-informative.
Mauve alignment generated an identity matrix which the identity scores range between 0 and 1, where 0 indicates that no identical homologous nucleotides were found, and 1 indicates that every homologous nucleotide was identical.
The CNS data set produced has the advantages of having been the object of some study, and because this data set depends on local alignments generating an even-handed sampling of conserved noncoding regions no matter how far they may exist from any conserved coding sequence.
The output BAM file, a standard format for sequence alignment, generated by a short read aligner may be created in different locations, or the output may not be stored in BAM at all.
In every case, both methods started from an identical 'ideal' sequence alignment, generated from a structure alignment between the template and the native target structure.
