Gpuccio: Functional Information Methodology

[gpuccio]

@glipsnort

Consider a cartoon piece of sequence that is 100 bp in length. The sequence has a function, every basepair contributes to the function, and loss of the function is lethal to the organism. 0.1% of all randomly chosen sequences could serve the same function equally well. This means the sequence has 7 bits of FI, correct? 300 different sequences can be reached from the functional sequence by one single-base substitution – which is the only kind of mutation in this cartoon world. The most likely case, then, is that all 100 bases will be conserved through evolution. Will blast return a bitscore of 7 bits for a 100 bp exact match?

ETA: Sorry, that’s 10 bits – I was taking the natural log.

I don’t follow your reasoning.

A sequence of 100 bp where each bp must be specific for the function to be present has, of course, a FI of 200 bits:

Target space = 1

Search space = 4^100

Target space/Search space = 6,22302E-61

FI = 200 bits

The FI expresses the probability of finding the target space from an unrelated state in one attempt. In this case, it is 1:4^100

I don’t follow your reasoning.

Of course, the perfect conservation of that sequence would inform us that the sequence has 200 bits of FI. Indeed, the bitscore of a 100 bp sequence against itself is 185 bits. Which seems good enough.