Finding Regions Of 100% Conservation

Question

[laukaitis.e]

I have a 36-row single alignment of a protein sequence, and I'm looking for regions with 100% conservation. How can I do so without resorting to simple visual methods?

I'm working with Biopython and ClustalOmega at the moment.

Answer 1

[David Westergaard]

Transpose your alignment and count the occurrence of each residue. For the latter you can use the python collections.Counter function, if you're lazy.

Answer 2

[always_learning]

If you are aware about perl then this may help you

Per-column conservation of multiple alignment in Perl