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How to find a specific sequence pattern in a fasta file?


 
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# 1  
Old 11-29-2019
How to find a specific sequence pattern in a fasta file?

I have to mine the following sequence pattern from a large fasta file namely gene.fasta (contains multiple fasta sequences) along with the flanking sequences of 5 bases at starting position and ending position,
Code:
AAGCZ-N16-AAGCZ
Z represents A, C or G (Except T)
N16 represents any of the four bases including A, T, G or C and these four base combination should have the length of 16 bases.

I have a fasta file as follows,
gene.fasta
Code:
>dox
ATGCTATGATAGTAGTAGATAGAGAGAGAGATAGATAGAGAGATAGATAG
>cyclin
ATGAGATAGAAAGCCATAGATAGTAGTAGATAAGCATATAGATAGATAGTAGTGATA
>fyl
TAGTAGTAGATAGATAGATGCGTACTGCTGATGATAGATGATAGATAGATAGATTAGAT
>tubulin
TAGATAGAAAGCAATAGATAGAACAAGATAAGCCTAGTCGTAGATGATAGATAG

The expected output should be like this,
Code:
>org1_1
ATAGAAAGCCATAGATAGTAGTAGATAAGCATATAG
>org1_2
ATAGAAAGCAATAGATAGAACAAGATAAGCCTAGTC

In order to mine the above mentioned pattern, I have used grep command but, I do not know how to specify only 3 bases for Z and also I could not specify N16 criteria in the grep command line. In addition to this, I do not know how to mine the 5 of the flanking bases along with the pattern. So kindly help me in this regard.
Thank you in advance.

Last edited by dineshkumarsrk; 11-29-2019 at 08:15 AM..
# 2  
Old 11-29-2019
How about (given there are only A, C, G, T in the fasta sequences, so no test for other chars needed)
Code:
grep -oE ".{5}AAGC[^T].{16}AAGC[^T].{5}" file
ATAGAAAGCCATAGATAGTAGTAGATAAGCATATAG
ATAGAAAGCAATAGATAGAACAAGATAAGCCTAGTC

This User Gave Thanks to RudiC For This Post:
# 3  
Old 11-29-2019
If you also want to print the >id then you can do it with perl:
Code:
perl -ne '/^>.*/ and $id=$&; /.{5}AAGC[^T].{16}AAGC[^T].{5}/ and printf "%s\n%s\n",$id,$&' gene.fasta

This User Gave Thanks to MadeInGermany For This Post:
# 4  
Old 11-29-2019
Can it occur only once per sequence? If not what should happen with multiple matches per sequence?

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