Hi all,
Are there any strong books or tutorials on the concepts underpinning manual inspection and editing of alignments garnered by our alignment algorithms? Applying to both pairwise and MSAs, and I know the difference is perhaps stark between the two, though not sure.
Warm regards,
Michael
Once you rely on visual inspection I think most people simply look at it in a program that colors the bases (or amino acids) and then want things to "line up" vertically. Of course this is subjective and therefore not a great thing to do. It would be better if people looked at this quantitatively, e.g. divergence levels, how many gaps, etc.
Fair enough, I was thinking, maybe it’s best to
automate the process of running local alignments (subsequent to an initial global pairwise or MSA) until the quality of the global alignment cannot be improved. I think there’s some rationale when going it manually though, like taking into account the sterics of certain aminos and using that knowledge to move them from one side of a series of gaps to the other maybe?
Can you explain further on gap number, divergence, etc? What about “gaps on the ends” as a principle, what underpins that? Any books out there that explain visual alignment?
Look out for
1. "Messy" alignments due to the hypervariable regions
2. in-frame stop codon
3.Any ambiguity in the aligned regions
5.No superfluous Gaps
Michael, a few questions to help get a better understanding of your needs:
1. What alignment algorithms / software tools have you used to date?
2. Are you aligning only amino acid sequences, or nucleotide sequences as well?
3. What is the range of lengths of the sequences that you work with?
4. Do you expect the sequences to be highly similar in general, with a few mismatches and gaps here and there, or more highly diverged?
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