BIOINFORMATICS Problem that i am struggling to solve. Computation of Profile
1
0
Entering edit mode
16 months ago

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 • 1.3k views
ADD COMMENT
0
Entering edit mode

Hello meatmangler0!

It appears that your post has been cross-posted to another site: http://seqanswers.com/forums/showthread.php?p=237082#post237082

This is typically not recommended as it runs the risk of annoying people in both communities.

ADD REPLY
0
Entering edit mode

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?

ADD REPLY
1
Entering edit mode
16 months ago

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)

ADD COMMENT

Login before adding your answer.

Traffic: 1206 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6