Question: Primer Design with Biopython
0
gravatar for patri_0_2
5.6 years ago by
patri_0_20
Spain
patri_0_20 wrote:

Hi,

I have a FASTA seq and I would like to write a program in python able to read this fasta file
containing a cDNA sequence and design a primer that can be used to insert the cDNA in
a plasmid.

PLEASE HOW CAN I DO IT???

Thanks!

biopython python • 2.9k views
ADD COMMENTlink modified 5.6 years ago by Whetting1.5k • written 5.6 years ago by patri_0_20
2
gravatar for Whetting
5.6 years ago by
Whetting1.5k
Bethesda, MD
Whetting1.5k wrote:

In general you'll get more/better answers if you show what you have tried :)

That being said, I am pretty bored...

this should work

from Bio import SeqIO

for record in SeqIO.parse("my_fasta.fas","fasta"):
    print record.id, str(record.seq[:20]), str(record.seq[-20:].reverse_complement())

This prints out the name of the sequence, the first 20nt and reverse complement of last 20nt. These should amplify your cDNA just fine. If you want to use primer design algorithms, look into primer3 as implemented in bio-python.

ADD COMMENTlink modified 5.6 years ago by Alex Reynolds29k • written 5.6 years ago by Whetting1.5k
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