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Questions - biopython

Get ID and protein sequences in biopython

I have this code. from Bio import SeqIO for seq_record in SeqIO.parse("aminoacids.txt", "fasta"): print(seq_record.id) print(repr(seq_record.seq)) Output: NP_414584.1 Seq('MNT...
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arteagavskiy

python

sequence

biopython

fasta

Votes: 0

Answers: 1

Latest Answer

repr is not designed for doing final output. It's essentially a debug tool. What you have is a Seq object. You probably need to be doing: print(seq_record.seq) which uses the str method.
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Tim Roberts

Finding CDRs (sequence) by its definition

I am puzzling to find the CDRs by its definition. Definition is to be matched with the previous and next sequence pattern (known as prefix and suffix respectively) and the CDR is between them. Moreove...
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Hossain

python

bioinformatics

biopython

fuzzy-search

fuzzy-logic

Votes: 0

Answers: 0

Reading a sequence in pairs and increase the base by +1

I want to read a sequence Amino Acid Sequence ("ACDEFGHIKL") in a pair of predefined motif length lets say 3 and print it. output will be [ACD,EFG,HIK]. but next time I want to increase its ...
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shivam

python

machine-learning

biopython

Votes: 0

Answers: 3

Latest Answer

You can use the regex library to get the list of blocks: import re re.findall('...','ACDEFGHIKL') Another option is the textwrap library: from textwrap import wrap wrap('ACDEFGHIKL', 3) To complete,...
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joaopfg

Parsing Specific lines from a pdb file using python

is there a way to parse the BFactor of a protein from its PDB file using Biopython/python? I am trying with biopython but i am not able to fetch the b factor of the proteins of my interest.
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arinjoy datta

biopython

Votes: 0

Answers: 0

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