How to search for a specific sequene in the fasta file and get several lists according to the times of repeat
Hi there, could anyone help with searching for a specific sequence, say "GGATCC" in a fasta file? My problem is I use grep "GGATCC" myfile.fasta the header containing the genomic location is mission. Besides, can I also generate some lists where "GGATCC" appears 2 times, 3 times, etc.? Thanks for your help in advance.
• 4,250 views
•
link
written
by
bright602 •
0 answers
No answers yet.
Log in to answer this question.
More posts like this
-
Match a column to another file (grep/awk)
written by Nathan •
-
Extract origin location and name kmers from source sequence
written by vivek37373 •
-
Plot nucleotide diversity with multiple sequence alignment
written by asoundi96 •
-
grep only specific motif from whole protein sequence
written by Jason •
-
grep only specific motif from whole protein sequence
written by Jason •
-
Extract specific peptides from a FASTA file
written by ijvechetti •
-
Generating random DNA sequence and paired-end alignment
written by ThePresident
-
How to concatenate gene sequence?
written by buthercup_ch •
-
Unable to use biomaRt getSequence() query to get sequences using genomic coordinates
written by eromasko
-
UCSC Table Browser: redundant CDS sequences in generated fasta
written by lilla.davim
Hello bright602!
Questions similar to yours can already be found at:
We have closed your question to allow us to keep similar content in the same thread.
If you disagree with this please tell us why in a reply below. We'll be happy to talk about it.
Cheers!
Thanks. But there is little information on getting the lists according to the time of repeats.
use the standard linux tools to get this number like "sort|uniq -c "