high frequency subsequences

Question

[setschmann]

Hi I have a little problem I can't wrap my head around:

I have a FASTA file with relatively short reads (around 80bp) and I want to find high frequency subsequences of a maximum lenght of 15bp of this FASTA file.

So I would need a programm or cript that outputs those subsequences with their count.

Do you have any ideas?

cheers

Answer 1

[lieven.sterck]

you might want to have a look at Kmer counting tools such as JellyFish, KAT, ntCard and such