Top "Biopython" questions

Biopython is a set of freely available tools for biological computation written in Python.

Reverse complement of DNA strand using Python

I have a DNA sequence and would like to get reverse complement of it using Python. It is in one …

python list bioinformatics biopython dna-sequence
How to call module written with argparse in iPython notebook

I am trying to pass BioPython sequences to Ilya Stepanov's implementation of Ukkonen's suffix tree algorithm in iPython's notebook environment. …

python ipython bioinformatics biopython suffix-tree
biopython no module named Bio

FYI: this is NOT a duplicate! Before running my python code I installed biopython in the cmd prompt: pip install …

python python-3.x pip bioinformatics biopython
How to find a open reading frame in Python

I am using Python and a regular expression to find an ORF (open reading frame). Find a sub-string a string …

python python-3.x python-2.7 biopython
How do I convert the three letter amino acid codes to one letter code with python or R?

I have a fasta file as shown below. I would like to convert the three letter codes to one letter …

python r bioinformatics biopython
How do I set the PYTHONPATH on Cygwin?

In the Biopython installation instructions, it says that if Biopython doesn't work I'm supposed to do this: export PYTHONPATH = $PYTHONPATH':/…

python cygwin biopython
Using Biopython (Python) to extract sequence from FASTA file

Ok so I need to extract part of a sequence from a FASTA file, using python (biopython, http://biopython.org/…

python python-2.7 biopython fasta
Is there a function that can calculate a score for aligned sequences given the alignment parameters?

I try to score the already-aligned sequences. Let say seq1 = 'PAVKDLGAEG-ASDKGT--SHVVY----------TI-QLASTFE' seq2 = 'PAVEDLGATG-ANDKGT--LYNIYARNTEGHPRSTV-QLGSTFE' with given parameters substitution matrix : blosum62 gap …

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How to extract chains from a PDB file?

I would like to extract chains from pdb files. I have a file named pdb.txt which contains pdb IDs …

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Installing Biopython: ImportError: No module named Bio

trying to install Biopython on Fedora 21, Python 2.7. I've done the following [mike@localhost Downloads](17:32)$ sudo pip2.7 install biopython You are …

python fedora biopython python-install