Homology modeling using the SWISS-MODEL server [41] coupled with alignments of known structures guided the strategic removal of flexible loops and helped define a reasonable subdomain division between the FtHPPK and FtDHPS modules.
The Pfam-A collection of multiple sequence alignments are produced by first establishing a hand-curated seed alignment of a couple of protein sequences from which a profile Hidden Markov Model is built which again is used to search for homologous sequences in primary sequence data bases.
There were some things I didn't like, like the alignment in a couple of places.
In fact, pairwise coarse alignment requires each couple of subsequent views in a dataset to possess a certain amount of overlap (from now on we address such requirement as the overlap constraint).
I think of how aligned we are as a team and how everyone shares certain values.There are a couple of things you need to have: natural alignment and connection".
By sequence alignment, we found that a couple of Arginine residues in Ash2L were highly conserved through evolution (square, Fig. S2).
For each gene fragment a couple of primers were designed on conserved regions identified based on alignments of barley and wheat EST (Additional file 1, Table S1).
Consequently, over the last couple of years, a small number of JavaScript-based sequence and alignment viewers have started to be developed.
Instead, he says, he has a "great alignment with the chairman", whom he meets every couple of weeks for a couple of hours.
Then he felt some discomfort a couple of weeks later and discovered that his back had been knocked slightly out of alignment.
