Multiple motif [available in .txt file ] search from large fasta file to find motif frequency then print fasta sequences
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9 weeks ago
Swarna • 0

Dear all,

I have a MOTIF.txt file contains MULTIPLE motifs (each line one motif, > 5000 MOTIFS)

for example

$ cat MOTIF.TXT
TCGFHAHH
GHHFDSJH

AND I HAVE A SEQUNCES.FASTA (> 10000 SEQUENCES) IN WHICH MOTIFS (MARKED BY BOLD AND ITALICS) MIGHT BE PRESENT AT ANY PLACE IN THE FASTA SEQUENCE

$ cat SEQUNCES.FASTA

>1
CCC***TCGFHAHH***
> 2
CC***TCGFHAH*H**GG
>3
TTT***GHHFDSJH***CC

NOW I WANT TO WRITE THE FREQUENCY OF MOTIF 1 (TCGFHAHH) THEN ALL THE FASTA SEQUNCES (INCLUDING HEADER) IN A NEW FILE. SIMILARLY FOR MOTIF2 IN THE SAME FILE AND SO ON

PLEASE HELP , SUGGEST HOW TO DO IT.

motif fasta frequency • 473 views
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No need to SHOUT.

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Use seqkit grep and/or seqkit locate (LINK).

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Thank you.

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