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BIOINFORMATICS Problem that i am struggling to solve. Computation of Profile

If anybody can answer this question i shall be grateful

Consider the following profile matrix Profile:

A: 0.4 0.3 0.0 0.1 0.0 0.9
C: 0.2 0.3 0.0 0.4 0.0 0.1
G: 0.1 0.3 1.0 0.1 0.5 0.0
T: 0.3 0.1 0.0 0.4 0.5 0.0

Compute Pr(TCGGTA|Profile). (Express your answer as a decimal and do not round your answer more than 5 decimal places.)

sequence genome homework
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updated by Jeremy Leipzig Jeremy Leipzig • written by meatmangler0 • meatmangler0

Also, this looks like directly copied from an assignment. While you got a good answer now, posting this like it is might be considered against our netiquette. In any case, you should check if you understand why the probabilities are calculated the way it is done. In addition, wouldn't it be more realistic to deal with log probabilities?

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written by Michael Dondrup Michael Dondrup

1 answer

This is a bit of R code to do this,

   options(digits=5)
probTable<-data.frame("A"=c(0.4, 0.3, 0.0, 0.1, 0.0, 0.9),
                      "C"=c(0.2, 0.3, 0.0, 0.4, 0.0, 0.1), 
                      "G"=c( 0.1, 0.3, 1.0, 0.1, 0.5, 0.0),
                      "T"=c(0.3, 0.1, 0.0, 0.4, 0.5, 0.0))

profileprob<-function(profile,probTable){
  profileVector=unlist(strsplit(profile,""))
  score=1
  for (eachBasePosn in (1:length(profileVector))){
   score=score*(probTable[eachBasePosn,profileVector[eachBasePosn]])
    }
  print(paste0("Probability score of profile",profile," is :",score ))
  }

profileprob(profile="TCGGTA",probTable)

For a new profile run it as profileprob(profile="TCGGTA",probTable)

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written by sure • sure

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