It interactively computes, displays and, upon modification of the target-template alignment, updates the multiple sequence alignments of the two protein families, their conservation score, secondary structure and solvent accessibility values, and local quality scores of the implied three-dimensional model(s).
This alignment updated the initial version of the B. rapa linkage map [ 16]. aBlocks expanded compared to the previous reports [ 27, 28] Most of the alignments between the linkage map and the Arabidopsis genome sequence were consistent with collinearity blocks previously inferred using sequenced markers with homology to single Arabidopsis genes [ 27, 28].
Therefore, to correct these erroneous annotations, we used Exonerate (Slater and Birney 2005) to align the corresponding protein sequences to the B. floridae reference genome (v2.0) (Putnam et al. 2008) and, based on the protein genome alignments, updated our copy of the GFF file.
DTBGE starts running with initial alignment and updates the template alignment with resulting eye movements and eyeball size frame by frame.
The sequence alignment, or updated versions thereof, is available at the Align-GVGD website [ 43].
The sequence alignment, or updated versions thereof, is available at the Align Grantham variation Grantham deviation (Align-GVGD) website [ 32].
As mentioned in the miRanda Algorithm section, the gap opening and extension costs, scoring matrices and alignment score update are different for the inside and outside seed regions.
The alignments were updated with additional proteins from GenBank to include five additional species (Homo sapiens, Mus musculus, Ornithorhynchus anatinus, Tribolium castaneum, and Caenorhabditis elegans).
In these cases, protein alignments were updated using the procedure described above, prior to final phylogenetic analyses (trees shown in Additional file 4).
Following the application of the selection rules, the result page (i.e., the similarity tree and individual pairwise alignments) is updated to account for changes in the list of the top-100 best BLAST.
It works as a dashboard for computing, displaying, inspecting and updating alignment related information in real time.
