What is an acceptable pairwise alignment % for a MSA

Question

[aframirez]

I am trying to work on a pipeline to generate optimize Multiple Sequence Alignments (MSAs) based on NCBI pulls. While I am doing this I am comparing how the length of alignments, consensus sequence, and pairwise % change and improve with each step.

It has lead to a question that I can't find a good reference to in the literature. What would you consider a good pairwise % for a MSA? I was thinking over 50%?

Open to thoughts and what you think are other benchmarks for a good and strong MSA

Answer 1

[Mensur Dlakic]

There is no pairwise alignment in MSA, because pairwise alignment by definition means that a pair of sequences is involved. There are many pairwise alignments between sequences in MSA - I assume this is what you are asking about.

If by good you mean a reliable alignment, over 50% identity may be a good target. If by good you mean an alignment between related sequences, there will be many related sequences from evolutionary distant organisms with pairwise alignment identities <50%, and probably all the way down to 30% would be reasonable.