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Locate short DNA sequence from fasta file

Hi guys. I'm beginner of bioinformatics.

In order to evaluate binding property of a compound which can selectively bind short DNA sequence in genome, I want to locate short sequence, for example "5'-GAATT-3'", from fasta file (genome) and make a heat map counting the number of the short sequence in windows. How should I do?

I'm not good at ruby or perl, and I'm glad if you give me solution in python, R or Linux command line.

genome blast
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updated by Matteo Schiavinato Matteo Schiavinato • written by Fumitaka Hashiya • Fumitaka Hashiya

Hi ,

If i resume you want to : -step 1 : "grep" all GAATT you have in you genome fasta -step 2 : note the coordinate of motif matching ? -step 3 : make a plot of you motif along your genome fasta ?

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written by Titus Titus

1 answer

fuzznuc helped me to solve the problem. Thank you very much!

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written by Fumitaka Hashiya • Fumitaka Hashiya

So you should to post the answer for the other !

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written by Titus Titus

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