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I have two fasta files. Each file contains sequences of short genomic regions in Rat or Mouse with a species-specific known SNP. 

File_1 :

>Rat_1
GGTGCCTGTGTATTGCCTCTGTCGACTGCCTTACGATGTGACCCGCTTCATGAT
>Rat_2
AAGCGGCCGGTTTCCTTGGCGACGAAGAGCGCGGGAATTTCAGATAGATTGTAATTGCGGCTGC
>Rat_3
GCAGCCATCTCTGCAACAATTGTGACAATGGCTGAGCCTAGCACAGACCCCAACAAAGAT


File_2 :

>Mouse_1
GGTGCCTGTGTATTACCTCTGTCGACTGCCTTACGATGTGACCCGCTTCATGAT
>Mouse_1_2
AAGCGGCCGGTTTCCTTGGCGTCGAAGAGCGCGGGAATTTCAGATAGATTGTAATTGCGGCTGC
>Mouse_1_3
GCAGCCATCTCTGCAACAATTGTGACAATGGTTGAGCCTAGCACAGACCCCAACAAAGAT

What I want to do is to find the SNP and extract about 20 bases around it. Result should look something like below...

Resut_file :

>Rat_1
CTGTGTATTGCCTCTGTC
         ^  
>Mouse_1
CTGTGTATTACCTCTGTC
         ^

Please, enlight me, programming masters!!!

Thank you.

mbk0asis
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  • This is not a specific programming question, you basically want us to write your program. Plus, we don't even know what an SNP is, that makes it hard to look for it. – chw21 Apr 27 '15 at 08:26

1 Answers1

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There are many tools for outputing the diff, like vimdiff, diff etc.

Try to have a look to similar question here

P.S. Asking such a question here is not relevant, you have to show at least what you have tried to do.

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deimus
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