Download and Installation
For Windows we provide click-and-run installers. Most Linux distributions will include an optional Biopython package (although this may be out of date). Otherwise you typically download and uncompress the archive, and install from source. See our downloads page for details including the prerequisites.
You can check your installation has worked at the python prompt:
>>> import Bio
If that gives no error, you should be done. If you get something like "ImportError: No module named Bio" something has gone wrong.
Try executing this in python:
from Bio.Seq import Seq,translate #create a sequence object of some DNA my_seq = Seq('CATGTAGATAG') #print out some details about it print 'seq is %i bases long' % len(my_seq) print 'reverse complement is %s' % my_seq.reverse_complement().tostring() #or see the whole record print 'sequence record:', my_seq #translate the sequence into a protein my_protein = translate(my_seq) print 'protein translation is %s' % my_protein.tostring() print 'protein record:', my_protein
You should get the following output:
seq is 11 bases long reverse complement is CTATCTACATG sequence record: Seq('CATGTAGATAG', Alphabet()) protein translation is HVD protein record: Seq('HVD', HasStopCodon(IUPACProtein(), '*'))
Reading and writing Sequence Files
If you are using Biopython 1.43 or later, try out the new SeqIO module.
- Learn how to program in Python
- Browse the Biopython Tutorial
- Examine the Class Diagram if you'd like to know more about the relationships between the modules.
- Use the Wiki Search tools to find more information on specific topics.