Question: MSA scoring tools/scripts
1
gravatar for jrj.healey
4 months ago by
jrj.healey2.6k
United Kingdom
jrj.healey2.6k wrote:

Does anyone know of any tools/scripts that would score a MSA in a sliding window manner?

I want to get the average identity across the length of an operon MSA, so I'm looking for something that gives me back a measure of conservation that I can graph.

I found some old threads on BioStars, but a lot of the linked packages either aren't exactly what I'm looking for, or the links etc are just defunct.

If I have to write this myself (probably with python), does anyone have any thoughts on appropriate ways to score each window?

msa alignment python • 196 views
ADD COMMENTlink modified 4 months ago • written 4 months ago by jrj.healey2.6k
3

Would Shannon entropy plot be helpful?

Just a thought.

Entropy From A Multiple Sequence Alignment With Gaps

ADD REPLYlink written 4 months ago by b.nota3.6k
1

Link looks helpful, thanks. Interesting idea to quantify the uncertainty instead of the conservation. Kinda the inverse of my initial thought process but would show the same end result I think.

ADD REPLYlink written 4 months ago by jrj.healey2.6k
3
gravatar for jrj.healey
4 months ago by
jrj.healey2.6k
United Kingdom
jrj.healey2.6k wrote:

Wrote my own in the end. Uses some bits of code I found online, but a bit more performant.

ADD COMMENTlink written 4 months ago by jrj.healey2.6k
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