Assignment 6: Motif Findinggenetics.wustl.edu/bio5488/files/2017/03/Assignment-6-Review-.pdf · Assignment 6: Motif finding • Input • Promoter sequences • PWMs of DNA-binding

Assignment6:MotifFindingBio54882/24/173/24/17!!

ReviewJ

Assignment6:Motiffinding• Input• Promotersequences• PWMsofDNA-bindingproteins

• Goal• FindputativebindingsitesinthesequencesbyscanningthesequencesformatchestothePWM

• Output• Listofthelocationsandscoresofputativebindingsites

PWM Putativebindingsequence

Promoter

AssignmentTODOs

• DeterminethehighestaffinitybindingsiteforeachPWM• CalculatebyhandorwriteascriptJ

• Commenttheexistingcode• Commenttheuser-definedfunctionswithfunctiondocstrings

• Modifythescripttoscanthereversecomplementoftheinputsequence• Modifythescriptonlyreporthitsthathavescoresaboveagiventhreshold

• Scanpromoters(n=2)tofindputativebindingsitesforeachDNA-bindingprotein(n=2)

• Answerfollow-upquestions

TFScoringMatrix

Indexing

• Indexingissomewhatarbitrary;howeverit’simportanttofollowconventions:• Thestartpositionofafeatureissmallerthanthestopposition• Thecoordinatesarerelativetotheforwardstrand

UseToyDataSets!!!

ACGT

1000

1000

0010

012

Base

Position

Lookatourexamples/instructionssoyougiveustherightanswersJ