Assignment 6: Motif Findinggenetics.wustl.edu/bio5488/files/2017/03/Assignment-6-Review-.pdf ·...
Transcript of Assignment 6: Motif Findinggenetics.wustl.edu/bio5488/files/2017/03/Assignment-6-Review-.pdf ·...
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Assignment6:MotifFindingBio54882/24/173/24/17!!
ReviewJ
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Assignment6:Motiffinding• Input• Promotersequences• PWMsofDNA-bindingproteins
• Goal• FindputativebindingsitesinthesequencesbyscanningthesequencesformatchestothePWM
• Output• Listofthelocationsandscoresofputativebindingsites
PWM Putativebindingsequence
Promoter
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AssignmentTODOs
• DeterminethehighestaffinitybindingsiteforeachPWM• CalculatebyhandorwriteascriptJ
• Commenttheexistingcode• Commenttheuser-definedfunctionswithfunctiondocstrings
• Modifythescripttoscanthereversecomplementoftheinputsequence• Modifythescriptonlyreporthitsthathavescoresaboveagiventhreshold
• Scanpromoters(n=2)tofindputativebindingsitesforeachDNA-bindingprotein(n=2)
• Answerfollow-upquestions
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TFScoringMatrix
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Indexing
• Indexingissomewhatarbitrary;howeverit’simportanttofollowconventions:• Thestartpositionofafeatureissmallerthanthestopposition• Thecoordinatesarerelativetotheforwardstrand
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UseToyDataSets!!!
ACGT
1000
1000
0010
012
Base
Position
Lookatourexamples/instructionssoyougiveustherightanswersJ