Canal-U

3.4. Predicting all the genes in a sequence

We have written an algorithm whichis able to locate potential genes on a sequence but only on one phase because we are looking triplets after triplets. Now remember that the genes maybe located on different phases and on the two strands. It means that to retrieve all the genes on a genome we have to look on six different sequences, three phases on each strand. Let's looknow how we can deal with this kind of search. First we have to modify a little bit our algorithm so that instead of starting at position One, I want to introduce a variable, a parameter which could be One or Two or Three so that I can run this algorithm starting on position One, first phase, or on position Two, second phase,or on position Three, third phase. Of course if you have Four, it's still the first phase again so it's unnecessary to test the numbers Four and Five and soon, you have only threepossible phases.