Locate for pattern in protein sequence with Biopython

Question

[arunprasanna83]

Hello,

I am trying to find sequences that has a tripeptide. The tripeptide can have any other amino acids following it, except 'P'. I extracted them with the following way.

from Bio import SeqIO
RGD = [] 
for record in SeqIO.parse("input.fasta", "fasta"):
    rgd_count = record.seq.count('RGD')
    if rgd_count >= 1:
        RGD.append(record) 
SeqIO.write(RGD, "RGD_Proteins.fasta", "fasta")

How can I introduce regex in this such that, RGD(N) is fine except, RGDP ?

Thanks in advance.

AP

Answer 1

[WouterDeCoster]

You need the re module, see here for the documentation.