Progressive alignment builds up a final MSA by combining pairwise alignments beginning with the most similar pair and progressing to the most distantly related.
The slippery concrete surfacing, steep left-side ramps, center breakdown lane, and wide-open alignment built for high speeds all contributed to a high number of crashes.
The current alignment, built in the mid-1980s as a mostly two-lane freeway, continues east across rugged terrain to the city of Grass Valley, where it joins SR 49 on the Golden Center Freeway.
We can consider the pairwise alignment built form A3 and A5 as a representative of their ancestral gene A35.
Following the identification of G. vaginalis virulence factors, all the members of their ortholog groups were extracted, an alignment built using Muscle with default settings [ 73], and a hidden Markov model (HMM) constructed using the hmmbuild command.
We then removed the four retrieved sequences from the alignment, built a new profile consisting only of 18 CENP-M sequences and searched the non-redundant database using hmmsearch (Eddy, 2011).
Corruption of the PSI-BLAST alignment built from hits to the α-helical bundle is evidenced by a profile-based similarity search (HHsearch), which finds the α/β P-loop hydrolase domain with probability 98%.
The first 145 aminoacids (aa) of CAG were aligned to the 131 aa contained in the crystalized human CENP-B DBD using a combination of a global alignment built with ClustalW and two local alignments of the HTH regions built with hmmalign software (Finn et al. 2011) and the pfam profiles CENP-B_N and HTH_Tnp_Tc5.
Covariation provides an independent method for verifying the quality of an alignment and should therefore be especially useful for verifying alignments built on sequence conservation alone.
