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The optional module utilizes a multiple sequence alignment (MSA) comprised of available reference genomes for the target.
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A large proportion of these algorithms utilize sequence conservation within a multiple sequence alignment (MSA) of homologous sequences to identify intolerant substitutions, for example, a substitution falling within a conserved region of the alignment is less likely to be tolerated than a substitution falling within a diverse region of the alignment (see reference [ 40] for a review).
However, rather than utilize the MFE structure of our initial sequence as the reference structure, we utilize a structure that is derived from a multiple sequence alignment (MSA) of homologous RNAs to more accurately reflect the biologically relevant structure [ 41].
Sequences from each species were further checked by carrying out a multiple sequence alignment and phylogenetic tree estimation with PASTA76.
Edgar, R. C. MUSCLE: a multiple sequence alignment method with reduced time and space complexity.
(A) Multiple sequence alignment of C. tritonis echotoxin and with echotoxins from other species.
Edgar, R.C. MUSCLE: a multiple sequence alignment method with reduced time and space complexity.
- Produces a multiple sequence alignment (MSA).
A multiple sequence alignment is essential.
They align a sequence to a multiple sequence alignment.
For most sequences this was a contiguous region, which was then utilized for multiple sequence alignment.
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