assignment 7: synthetic...
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Assignment7:SyntheticBiology
March3,2017
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GeneSynth
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GoalofAssignment
• Designprimerstosyntheticallyconstructanovelpeptide.• UseRecursiveFunctiontogenerateprimersequences
• Narrowdownprimersbasedonpreferredannealingtemperaturesandbyavoidingparticularrestrictionsites.• Booleansareadatatypewithtwovalues,TrueandFalseinpython.• Whenyouareusingan“if”statementyouarereallyevaluatingwhetherastatementisTrueorFalse.
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Codontable
SincesomeAAshavemultiplecodonsequences,thecodemustbeabletogenerateallcombinationofsequencespossible.
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BooleanExamples
>>>A=1ifA==1:(evaluatestoTrue)Dosomething
else:(abovewasFalse)Dosomethingelse
>>>A=10whileA>5:(EvaluatestoTruewhenAis10,9,8,7,6)(FalsewhenA=5)Print(A)A=A-1
>>>A=1A==2 evaluates toFalseA>1evaluates toFalseA<1evaluates toFalse0<Aevaluates toTrueTrueand Trueevaluates toTrueTrueand False evaluates toFalseFalse andFalse evaluates toFalseTrueand Trueevaluates toTruenotFalse evaluates toTruenotTrue evaluates toFalseFalse orTrueevaluates toTrueFalse orFalse evaluates toFalseTrueorTrue evaluates toTrue
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Usingbooleans ->identifyparticularsequences
AnyandAllallowyoutosee ifastringappears inanotherstringorlistordictionary.• Anyactsasan“or”soFalseorFalseorTrueevaluatestoTrue.• Allactsasan“and”soFalse andFalseandTrueevaluates toFalse.
*Anytime aTrue isinan“or”statement,wholestatement isTrue.*Anytime aFalse isinan“and”statement,wholestatement isFalse.
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Howtocalculatemeltingtemperature
MT=64.9+(41.0*(#G+#C- 16.4)/Lengthofoligo)
• Allprimersmustbewithin0.5degreesof58.0degreesCelsius!• Couldwriteanotherfunctionthatchecksforthis:
ie.def meltingtemp(DNA_seq):
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Yourassignment
• Youaregivenafunction(PolkCode)thatconvertsaminoacidsequencestoallpossiblenucleotidesequences.• Given3AAsequences,youneedtofindnucleotideoutputsbasedwithinacertaintemperaturerangewithsequencerestrictions.• YourcodewilltakeAAsequence(s)andmeltingtemperature(Tm)asinputandoutputallnucleotidesequencesmeetingthecriteria.•Considermakingyourcodesothatincantakeanynumberofinputs.
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Requirements
•DueWednesday(3/22/16) beforeclass.•Yoursubmissionfoldershouldcontain:
• modified Polk.py script(cantake ineither2ormorearguments)• README.txt filewithinstructions onhowtorunyourprogramandatableoftheDNAstrings andtemperatures foreachAAinputted.
• ShouldprintPrimersequences andMelting Temperature• Remembertocommentyourscript!