Getting Started

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==Beginners==
 
==Beginners==
  
* Learn how to program in [[Perl]], see several [[Tutorials]]
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* Learn how to program in [http://www.python.org Python]
** [http://stein.cshl.org/genome_informatics/ Genome Informatics]
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** [http://swaroopch.info/text/Byte_of_Python:Main_Page A Byte of Python]
** [http://www.perlmonks.org/index.pl?node=Tutorials PerlMonks Tutorials]
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** [http://www.diveintopython.org/toc/index.html Dive Into Python]
** [http://www.perl.com/cs/user/query/q/6?id_topic=74 Perl.com tutorials]
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* Browse the [http://biopython.org/DIST/docs/tutorial/Tutorial.html Biopython Tutorial]
** [http://www.ebb.org/PickingUpPerl/ Picking up Perl]
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* Examine the [http://biopython.org/DIST/docs/api/public/trees.html Class Diagram] if you'd like to know more about the relationships between the modules.
** [http://learn.perl.org/ Learn Perl]
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* Read the {{HOWTO|Beginners}}
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* Browse the [[Bptutorial|Bioperl Tutorial]]
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* Examine the [[Class Diagram]] if you'd like to know more about the relationships between the modules.
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==Further reading==
 
==Further reading==

Revision as of 21:46, 19 January 2007

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

Contents

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

Further reading

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