Primer Design with Biopython

Question

[patri_0_2]

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!

Answer 1

[Whetting]

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.