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


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


biopython entrez sequence • 241 views
ADD COMMENTlink written 9 months 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 9 months ago by Sej Modha4.7k

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


ADD REPLYlink written 9 months ago by paumarc10

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

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

See more on the BioPython webpages:

ADD REPLYlink modified 9 months ago • written 9 months ago by Sej Modha4.7k
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