assignment 6: motif findinggenetics.wustl.edu/bio5488/files/2017/03/assignment-6-review-.pdf ·...
TRANSCRIPT
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