Question

How to retrieve all pentamer from a sequence?

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6.3 years ago

vmicrobio ▴ 290

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!

pentamer motif sequence • 977 views

ADD COMMENT • link updated 6.3 years ago by GenoMax 141k • written 6.3 years ago by vmicrobio ▴ 290

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6.3 years ago

GenoMax 141k

kmercountexact.sh from BBMap suite should work as well.

ADD COMMENT • link 6.3 years ago by GenoMax 141k

score 2 · Accepted Answer · 2018-01-10

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6.3 years ago

5heikki 11k

You can do this with e.g. Jellyfish

ADD COMMENT • link 6.3 years ago by 5heikki 11k

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

ADD REPLY • link 6.3 years ago by vmicrobio ▴ 290

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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 REPLY • link 6.3 years ago by 5heikki 11k