Getting Started
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#create a sequence object of some DNA | #create a sequence object of some DNA | ||
| − | my_seq = Seq('CATGTAGATAG') | + | my_seq = Seq.Seq('CATGTAGATAG') |
#print out some details about it | #print out some details about it | ||
Revision as of 23:47, 18 December 2007
Contents |
Download
Installation
Tutorial
The Biopython Tutorial and Cookbook (HTML, PDF) contains the bulk of our documentation. See Documentation for more links.
Quick example
Executing this:
from Bio.Seq import Seq,translate #create a sequence object of some DNA my_seq = 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
Produces:
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.
Beginners
- 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.
Further reading
- Use the Wiki Search tools to find more information on specific topics.
