Next, is a description of the extensive data collection effort that utilized differential cinematic GPS surveys to define the horizontal alignment variables, and road safety inspections (RSIs) to quantify the other road characteristics related to safety.
ChromA provides a number of visualizations for alignments, variable data and chromatograms, which are generated using the open source library JFreeChart (Gilbert and Morgner, 2009).
In the protein alignment, 11 variable residues are VirB4a-specific, whereas 43 variable residues are unique to VirB4b, illustrating more conservation of VirB4a with non-Rickettsia proteins.
Although the characteristic TIRs and TSDs of the five β-amylase elements are easy to align, the regions between the TIRs (excluded from Fig. 1 alignment) are variable in both length and sequence (Fig. 2).
The primers were designed, by multiple sequence alignment of variable regions, specific for cold-adapted donor virus HTCA-A101, as compared to other influenza A viruses.
Additional file 5: Alignment of variable domains from SCAmpPs-3 and -4 promoters 130 bp 5′ to the transcription start.
CDD [ 46] provides a collection of PSSM profiles for Pfam families and MulPSSM [ 47] is another related resource that use multiple PSSMs corresponding to a given alignment and variable reference sequences.
The program snp-sites was then used to code missing data and SNP sites from ambiguous sites within the consensus sequences and create an alignment containing variable sites (https://github.com/andrewjpage/snp_sites).
Strong between- and/or within-population differentiation of haplotypes indicative of local or partial selective sweeps are observed in the alignment of variable sites in candidate genes harboring the strongest signals (e.g. Additional file 8: Figure S8).
Eighty-one of the 343 total codons in the alignment were variable at the amino acid level and, of these, 27 were identified by BEB analysis as members of the divergently evolving site class under the best fitting 'CmC αβMVR & βT' model (PP > 0.75 for each site) (Table 5).
Valimaki et al. (2007) have previously explored the use of BWT compressed self-index methods for efficient compression and search of genetic sequence data from many individuals, but this does not require a fixed alignment of variable sites as in the work presented here, and is substantially different.
