Getting Started

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(Quick example: Don't need tostring() any more, also I wanted to include a stop codon)
m (Quick example: Use translate method)
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Try executing this in python:
 
Try executing this in python:
 
<python>
 
<python>
from Bio.Seq import Seq,translate
+
from Bio.Seq import Seq
  
 
#create a sequence object of some DNA
 
#create a sequence object of some DNA
Line 27: Line 27:
 
print 'seq %s is %i bases long' % (my_seq, len(my_seq))
 
print 'seq %s is %i bases long' % (my_seq, len(my_seq))
 
print 'reverse complement is %s' % my_seq.reverse_complement()
 
print 'reverse complement is %s' % my_seq.reverse_complement()
 
+
print 'protein translation is %s' % my_protein.translate()
#translate the sequence into a protein
+
my_protein = translate(my_seq)
+
 
+
print 'protein translation is %s' % my_protein
+
 
</python>
 
</python>
  

Revision as of 22:21, 15 January 2009

Contents

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 Most Linux distributions will include an optional Biopython package (although this may be out of date).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.

Tutorial

The Biopython Tutorial and Cookbook (HTML, PDF) contains the bulk of our documentation. See Documentation for more links.

Quick example

Try executing this in python:

from Bio.Seq import Seq
 
#create a sequence object of some DNA
my_seq = Seq('CATGTAGACTAG')
 
#print out some details about it
print 'seq %s is %i bases long' % (my_seq, len(my_seq))
print 'reverse complement is %s' % my_seq.reverse_complement()
print 'protein translation is %s' % my_protein.translate()

You should get the following output:

seq CATGTAGACTAG is 12 bases long
reverse complement is CTAGTCTACATG
protein translation is HVD*

Reading and writing Sequence Files

If you are using Biopython 1.43 or later, try out the new SeqIO module.

Beginners

Further reading

  • Use the Wiki Search tools to find more information on specific topics.
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