PAM vs BLOSUM score matrices
Amino acids, nucleotides or any other evolutionary character are replaced by others at some rate. For example, imagine an evolutionary sequence with three po...
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Expected values of score matrices
There are many ways to compute score matrices for amino acid alignment. Typically score matrices are based on the log-odds of amino acid replacements, and so...
Smith–Waterman
The Smith–Waterman algorithm is basically the Needleman–Wunsch, but with a few modifications to turn it into a local alignment algorithm. These are:
Needleman–Wunsch
Global alignment algorithms are used to align two globally similar sequences. Commonly global alignment is used to identify first whether two protein, DNA or...
Recursion
Recursion is where a single function inside a computer program calls itself. This turns out to be an extremely versatile tool in the computer science toolbox...