Getting Started

Revision as of 21:42, 19 January 2007

--Jblucks 16:36, 19 January 2007 (EST): This page modeled after the one for bioperl

Download

See Getting BioPython

Installation

See Installing BioPython

Quick example

Executing this:

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

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(), '*'))

Beginners

• Learn how to program in Perl, see several Tutorials
  • Genome Informatics
  • PerlMonks Tutorials
  • Perl.com tutorials
  • Picking up Perl
  • Learn Perl
• Read the Template:HOWTO
• Browse the Bioperl Tutorial
• Examine the Class Diagram if you'd like to know more about the relationships between the modules.

Further reading

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