Question: Probability of having same starting base on complementary strands
0
gravatar for banerjeeshayantan
4 weeks ago by
banerjeeshayantan10 wrote:

So this question came up in a lecture on "Introduction to transcription". Our professor asked, what is the probability of having the same starting base on the forward and the reverse strand. In other words, if I have

5'_______3'  
ATTGCCATAT  
TAACGGTATA  
3'_______5'

What are the odds of that happening? (same for other bases, T,G,C) My answer is as follows:
P(A)=P(T)=P(G)=P(C)=1/4 So, P(Aon5' and Aon3')=P(A).P(A) =1/16
and, P(Gon5' and Gon3')=P(G).P(G)=1/16, and going on like this, we add up (for all bases) and get 1/4. Am I correct?
The issue here is this fact: The probability of having same base on reverse strand =1/4 = Probability of having any one base
Is there any significance to this?

sequence • 168 views
ADD COMMENTlink modified 4 weeks ago by Devon Ryan70k • written 4 weeks ago by banerjeeshayantan10
1

This model assumes that the p for each base is 1/4. Coming from a biological standpoint, transcription (start) sites are highly clustered by binding motifs, so by far not a random distribution of nucleotides. To have it accurately, one probably needs to correct for factors like GC content. So I would say a naive probability as you propose will not be accurate. Maybe you have a look at papers about motif enrichments and how they model nucleotide occurrence.

ADD REPLYlink written 4 weeks ago by ATPoint1.1k

Thanks for replying. Will look into factors like GC content.

ADD REPLYlink written 4 weeks ago by banerjeeshayantan10
2
gravatar for Devon Ryan
4 weeks ago by
Devon Ryan70k
Freiburg, Germany
Devon Ryan70k wrote:

Yes, assuming equal probability bases, the probability of having a base and its complement at opposite ends of a given interval is 25%. Yes, this is because the probability of any base is 25% and would be different otherwise. Of course this is unlikely to match what happens in any organism for the reasons ATPoint mentioned.

ADD COMMENTlink written 4 weeks ago by Devon Ryan70k

Thanks for clearing.

ADD REPLYlink written 4 weeks ago by banerjeeshayantan10

By curiosity , what is other bias to consider for this kind of problem ?

Is there influences of genetic code ? (i thought about proportion of base on codon position )

ADD REPLYlink written 4 weeks ago by Titus400

The proportion of a base on a strand needn't equal the proportion at a given end of some interval (consider transcription factor binding sites as an example where this is very much not the case).

ADD REPLYlink written 4 weeks ago by Devon Ryan70k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 564 users visited in the last hour