Question: find position of 3' utr at entrez
0
gravatar for paumarc
17 days ago by
paumarc10
Barcelona (ICO)
paumarc10 wrote:

Hi

I am using the BIOPYTHON library Bio to retrieve sequences from Entrez, I need to know the ending position of 5' UTR and the starting position of 3' UTR. How do I get them?

thank you

p

biopython entrez sequence • 74 views
ADD COMMENTlink written 17 days ago by paumarc10

Are you fetching the records in the Genbank format? If yes then you can parse the features to identify the UTR tags.

ADD REPLYlink written 17 days ago by Sej Modha4.4k

Can you tell me any example of how to get or tutorial them? it is driving me mad

thanks

ADD REPLYlink written 17 days ago by paumarc10

Following code can be modified to check for UTR instead of CDS for example:

from Bio import SeqIO
records = SeqIO.parse("sequence.gb", "genbank")
for seq_record in records:
    for feature in seq_record.features:
        if 'CDS' in (feature.type):
            if 'methyltransferase' in str(feature.qualifiers["product"]):
                print(feature.qualifiers["locus_tag"],feature.qualifiers['product'])

See more on the BioPython webpages: http://biopython.org/DIST/docs/tutorial/Tutorial.html#htoc130

ADD REPLYlink modified 17 days ago • written 17 days ago by Sej Modha4.4k
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