Notice
4.5. A sequence alignment as a path
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Descriptif
Comparing two sequences and thenmeasuring their similarities is an optimization problem. Why? Because we have seen thatwe have to take into account substitution and deletion. During the alignment, the comparison of the two sequences, we haveto insert blank characters at a certain position in order tohave an optimal score that is we want the sequence to be themore similar as possible. So the problem is to find whereto locate the blank character. There are many solutions and wewant to find the best one, it is an optimization problem. How do we deal with thisoptimization problem? We will consider an alignmentbetween two sequences as a path in that kind of grid. Here we havethe characters of the first sequence and there, the charactersof the second sequence. The path starts from this nodeand must arrive on that node. What are the rules of the game? You may have unitary path likethat or like that or like that, along, horizontal or vertical linesor diagonal lines and so on. The idea is to arrive to the lastnode and we'll see that the "S" corresponds to one alignment,one possible alignment between these two sequences. Why? Simply because drawing a diagonallike that means taking into account a substitution. Thisis the first sequence.
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