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Calculate percentage of sequence identity between two RNA sequences using Infernal

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

rna alignment
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updated by Ram Ram • written by sri • sri

1 answer

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

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updated by Ram Ram • written by nawrocke • nawrocke

Hello Eric. That worked like a charm. Thanks!

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written by sri • 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?

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written by sri • sri

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