Hi,
I wish to identify unique amino acid subsequences in a MSA for a sequence of interest.
Example:
A = Sequence of interest
A:NYTPLUYB
B:NYPNLUYB
C:NYPNLUYB
Here in A sequence 'TP' are the unique amino acids. I am looking for a tool/package that can automatically detect these unique patterns. Any suggestion will be highly appreciated.
•
written
by
sushmitapaul007 •
1 answer
There is a python script that will calculate conservation scores from the alignment:
https://github.com/Cantalapiedra/msa_conservation_index
Most people want to detect the conservation rather than a lack of it, but it should still work for your purpose after you pick a conservation threshold.
What also might work for you is to use a MSA viewer and color the sequences according to strict conservation. In that case residues that are not conserved will not be colored.
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I guess you are after single-copy K-mers in those strings, which in fact don't need to be aligned, right?