how to evaluate protein motif conservation?

Question

[biolab]

Dear all,

I have numerous cross-species protein motif alignment. How to calculate the conservation scores? An example is shown below. Is it possible to simply score : as 1 and . as 0.5? This way to some extent shows conservation extent. THANKS A LOT for any of your advices and answers!

ILRYLARKHH
:: ::: :..
ILSYLAAKYN

Answer 1

[Manvendra Singh]

There is very nice method called CS Method http://conscore.embl.de/CS.wsdl which was published in http://www.biomedcentral.com/1471-2105/9/229

you can try it if you like.

[biolab]

Hi Manu, thanks a lot for your comments!