Question: How to retrieve all pentamer from a sequence?
0
gravatar for vmicrobio
15 months ago by
vmicrobio240
vmicrobio240 wrote:

Hi all!

Does anyone have an idea on how to get a list of pentamer motifs and the number of time they are found in a given sequence?

That would help me a lot, thanks in advance!

motif sequence pentamer • 328 views
ADD COMMENTlink modified 15 months ago by genomax65k • written 15 months ago by vmicrobio240
2
gravatar for 5heikki
15 months ago by
5heikki8.4k
Finland
5heikki8.4k wrote:

You can do this with e.g. Jellyfish

ADD COMMENTlink written 15 months ago by 5heikki8.4k

this software is awesome, that's exactly what I was looking for, you made my day!!

ADD REPLYlink written 15 months ago by vmicrobio240

That's nice to hear. Be sure to read the manual so you know what a canonical k-mer is. Or just see here

ADD REPLYlink modified 15 months ago • written 15 months ago by 5heikki8.4k
1
gravatar for genomax
15 months ago by
genomax65k
United States
genomax65k wrote:

kmercountexact.sh from BBMap suite should work as well.

ADD COMMENTlink written 15 months ago by genomax65k
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