First of all, this is not a question about alignment, but more about string matching/searching, but it might be related.

My problem is in the following image, but I don't know what's its name.

Here P = 'agcga'.

The problem is defined as follows:

Input: string P length m, string T length n (P is a short sequence, N is a long genome)

Algorithm: for each position i in [0..n-m], compute res[i] = sum(P==T[i:i+m])

                   In other word, res[i] = the number of equal characters between P and T[i:i+m]

Output: array res[i]

Does anyone know the name of this problem? Or is it never used anywhere?

If it is used, then what's the current method to calculate res[] ?

Thank you.



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