Locate short DNA sequence from fasta file

Question

[Fumitaka Hashiya]

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.

[Titus]

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 ?

Answer 1

[Matteo Schiavinato]

This might be what you want: http://emboss.sourceforge.net/apps/cvs/emboss/apps/fuzznuc.html

However, spend some time reading this: How Do I Search A Genome For A Known Motif, And Get An Interval File Of All Instances Of The Motif?

[Fumitaka Hashiya]

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

[Titus]

So you should to post the answer for the other !