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BioPython Tutorial
Chapter1
Introduction
1.1
WhatisBiopython?
TheBiopythonProjectisaninternationalassociationofdevelopersoffreelyavailablePython(http://www.
python.org)toolsforcomputationalmolecularbiology.Thewebsitehttp://www.biopython.orgprovides
anonlineresourceformodules,scripts,andweblinksfordevelopersofPython-basedsoftwareforlifescience
research.
Basically,wejustliketoprograminpythonandwanttomakeitaseasyaspossibletousepythonfor
bioinformaticsbycreatinghigh-quality,reusablemodulesandscripts.
1.1.1
WhatcanIfindintheBiopythonpackage
ThemainBiopythonreleaseshavelotsoffunctionality,including:
•Theabilitytoparsebioinformaticsfilesintopythonutilizabledatastructures,includingsupportfor
thefollowingformats:
–Blastoutput–bothfromstandaloneandWWWBlast
–Clustalw
–FASTA
–GenBank
–PubMedandMedline
–ExPASyfiles,likeEnzyme,ProdocandProsite
–SCOP,including‘dom’and‘lin’files
–UniGene
–SwissProt
•Filesinthesupportedformatscanbeiteratedoverrecordbyrecordorindexedandaccessedviaa
Dictionaryinterface.
•Codetodealwithpopularon-linebioinformaticsdestinationssuchas:
–NCBI–Blast,EntrezandPubMedservices
–ExPASy–ProdocandPrositeentries
•Interfacestocommonbioinformaticsprogramssuchas:
5
–StandaloneBlastfromNCBI
–Clustalwalignmentprogram.
•Astandardsequenceclassthatdealswithsequences,idsonsequences,andsequencefeatures.
•Toolsforperformingcommonoperationsonsequences,suchastranslation,transcriptionandweight
calculations.
•CodetoperformclassificationofdatausingkNearestNeighbors,NaiveBayesorSupportVector
Machines.
•Codefordealingwithalignments,includingastandardwaytocreateanddealwithsubstitution
matrices.
•Codemakingiteasytosplitupparallelizabletasksintoseparateprocesses.
•GUI-basedprogramstodobasicsequencemanipulations,translations,BLASTing,etc.
•Extensivedocumentationandhelpwithusingthemodules,includingthisfile,on-linewikidocumen-
tation,thewebsite,andthemailinglist.
•IntegrationwithBioSQL,asequencedatabaseschemaalsosupportedbytheBioPerlandBioJava
projects.
WehopethisgivesyouplentyofreasonstodownloadandstartusingBiopython!