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Looking for a simple tool to match 6-mers (such as TGATCA) to motifs

Dear community,

I'm reaching out to find a simple tool that can do something like this: If I input TGATCA, it tells me it's the AP1 motif.

Can't believe I haven't found such a tool!

Best, Changxu

motif.
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updated by Pierre Lindenbaum Pierre Lindenbaum • written by changxu.fan changxu.fan

If I input TGATCA, it tells me it's the AP1 motif.

And where does this information come from i.e. TGATCA represents AP1 motif?

Can't believe I haven't found such a tool!

Is the said tool supposed to look this information up?

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written by GenoMax GenoMax

1 answer

If I input TGATCA, it tells me it's the AP1 motif.

the following awk script works as described above.

awk '($0=="TGATCA"){print "AP1"}' input.txt

or

grep -E '^TGATCA$' input.txt > /dev/null && echo "AP1"
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written by Pierre Lindenbaum Pierre Lindenbaum

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