gravatar for anasjamshed1994

2 hours ago by

I have one fasta file which has 30 sequences and pattern file which contain different motifs.

I need to match my motifs with fasta sequences and location in which it is authenticated should be highlight like this :

enter image description here

The script which I have developed until now :

# biopython
from Bio import SeqIO
# regex library
import re

# file with FASTA sequence
infile = r"C:UsersLenovoDesktopfnlpythPromoter Sequence.fasta"

# pattern to search for
iupac = 'GGCA'

# look through each FASTA sequence in the file
for seq_record in SeqIO.parse(infile, "fasta"):
    print ("Sequence ID: ",, "; ", len(seq_record), "bp")
    print (seq_record.seq)

    # scan for IUPAC; re.I makes search case-insensitive
    matches = re.findall( iupac, str(seq_record.seq), re.I)
    if matches:
        print ("Matches = ", len(matches))

I need help to complete this script?

Source link