We know BLAST can compare two sequences, however it compares sequences by lining up them. My question is can we shift one sequence then compare the other. Let me give you a simple example:the length is 15
GTTCCTAGTCTAGAC
TCCTAGTCTAGACTT
If we shift it and compare
GTTCCTAGTCTAGAC
|||||||||||||
TCCTAGTCTAGACTT
Then there are 11 letters hit, we define the score by 11/15=73%. Of course, we can shift to whatever we want. How to find the max score? Is there such a software to do it? Thanks.