Coin Flip: Variable decides between values

I have several RNA sequences:
gggagauuAGUCAU(g/c)UAAGuuUACAAUC(u/a)CGCuuGUA(g/c)AUCGUAGuuGU(u/a)GU
ggcgcuuuGAC(u/a)CUUCUGCuuauguccC(u/a)CUAuuCUUA(g/c)AUGACUuuGG(u/a)CC
ggcaacuugaucccUC(u/a)GGuuagcgccGG(u/a)CCuuucucccAC(u/a)ACuuCAC(u/a)G
gggaucuuACCUAC(u/a)CACGuuUGCUG(u/a)UCUCGuuGCAGAAG(u/a)GUCuuCC(u/a)GA
ggacauuuCGAGA(u/a)CAGCAuu(g/c)uuucccGACCuuGCG(u/a)GAUUGUAuuUAG(u/a)G
gggaaa(g/c)uuCGUG(u/a)GUAGGUuuguugccC(u/a)GUGuuCUACGAU(g/c)UACuuGGUC
You'll notice there are several instances of '(g/c)' and '(u/a)', where the nucleotide can be either G or C or either A or U.
I need print all the possible sequences that can be made from the above six. In other words, I need to implement a 'coin flip' that decides between C/G or A/U every time '(g/c)' or '(u/a)' appears. All-in-all there are over one million possible sequences.
How can I do this?

It doesn't seem to me that there will be millions of possible combinations. In fact, if I understand the problem correctly, I think there are two possible options for each of the a/u or g/c nucleotides. Since there are four of them in each of the six strings, each string has 2^4 possible permutations, or 16 Thus, the way I see it, you have 16*6 = 96 possible strings to work from. What I would do is enumerate these 96 strings, placing them into a list or collection of some kind. Then, you have the ability to use each of these strings as necessary to build up your overall RNA string.
If the final RNA string must be a combination of exactly 6 of these strings, with no repetition, then you have 96 *95 *94 *93 *92 *91 = 6,674,768,880, which might be (I suppose) where you got your original answer.
Assuming I understand this correctly, you probably don't want to enumerate all of these. What it seems like you're asking is how to simulate the possibility of randomness developing in the final RNA sequence. So, I think the problem is better stated like:
Given these 6 sequences of RNA, how can I build a single string such that at each possible (a/u) or (g/c) each of the possible choices has a 50% possibility of being present at that location?
If this is what you're looking for, then I think a better algorithm is to build the enumerations of the RNA strings such that the g/c and a/u choices are intact, and then begin traversing through it, each time you run the experiment, calculating a new random variable at each of the parenthesized points in the RNA string. This will not produce unique strings, but will be like a simulation of RNA construction.
Edited by: jwir3 on Jan 29, 2010 11:48 AM

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