Calculate percentage of sequence identity between two RNA sequences using Infernal

Question

[sri]

I'm just wondering whether we could calculate percentage of sequence identity between two RNA sequences using Infernal through the cmalign feature? If yes, how do I go about it? Any help is appreciated. Thanks

Answer 1

[nawrocke]

To calculate sequence percent identity using Infernal, first align the sequences of interest to the same model using cmalign. Then use the esl-alipid utility program that is included with Infernal here <PATH-TO-INFERNAL-1.1.1>/easel/miniapps/esl-alipid. For example:

/src/infernal-1.1.1/src/cmalign my.cm my.fa > my.stk
/src/infernal-1.1.1/easel/miniapps/esl-alipid my.stk

Let me know if you have further questions.

-Eric

[sri]

Hello Eric. That worked like a charm. Thanks!

[sri]

Eric, I just have one additional question. Let say, I have more than 1 .stk file. So would it be possible to calculate the sequence similarity of all the files at the same time? Or do I need to write a script to do that?