The phrase "alignment one can" is not correct and lacks clarity in written English.
It may be used in contexts discussing the ability or possibility of achieving alignment, but it requires additional context to be meaningful.
Example: "In this project, we will explore the alignment one can achieve through effective communication strategies."
Alternatives: "alignment that can be" or "alignment achievable by".
Given two aligned sequences (e.g. taken from the multiple sequence alignment), one can use a r×r divergence matrix F to represent the relative proportion of each of the possible character state pairs in the pairwise comparison of these two sequences (as schematized for DNA sequences by formula (19) in [ 11]).
There are many programs searching for homology and alignment; one can use them via the Internet.
From the alignment one can identify OTUs (desired result #1) and build phylogenetic trees (desired result #3).
In addition, if one has doubts about the correct alignment, one can test several alignments, prepare the corresponding models and score all of them with Rd.HMM.
Given the initial alignment one can estimate a CM as explained before to start the EM iteration.
Therefore, by comparing the average percentage of synonymous substitutions per codon between the CGFS class and the CPYC class GRXs in the conserved positions of each multiple alignment, one can obtain additional information regarding whether these proteins have been evolving for approximately the same time.
By evaluating these alignments, one can see how all consensus sequences constructed based on all dimeric CAP families align pattern3-to-pattern3 with the DTG/ILG template.
By performing extensive EST searches, in cycle order, and using multiple sequence alignment algorithms, one can sometimes reconstitute full-length cDNA clones.
The target and source dimensions and resolutions now are stored in the output alignment file, so that one can use inverse transformations if desired.
Upon job termination, the user is directed to the results page, where pairwise alignments are displayed and one can toggle between them, see Figure 2 (right).
– Given a polynomial time algorithm for finding a largest alignment of RMSD below a threshold d, one can efficiently compute an alignment of a given size ℓ which minimizes the RMSD (Theorem 7).
