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Finding Regions Of 100% Conservation

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.

alignment
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updated by always_learning always_learning • written by laukaitis.e • laukaitis.e

2 answers

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.

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written by David Westergaard David Westergaard

If you are aware about perl then this may help you

Per-column conservation of multiple alignment in Perl

• 0 views • link
written by always_learning always_learning

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