find position of 3' utr at entrez
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2.8 years ago
paumarc ▴ 20

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

sequence Entrez biopython • 667 views
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Are you fetching the records in the Genbank format? If yes then you can parse the features to identify the UTR tags.

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

thanks

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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

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