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PAM vs BLOSUM score matrices

5 minute read

Amino acids, nucleotides or any other evolutionary character are replaced by others at some rate. For example, imagine an evolutionary sequence with three po...

Expected values of score matrices

3 minute read

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...


3 minute read

The Smith–Waterman algorithm is basically the Needleman–Wunsch, but with a few modifications to turn it into a local alignment algorithm. These are:


16 minute read

Global alignment algorithms are used to align two globally similar sequences. Commonly global alignment is used to identify first whether two protein, DNA or...


1 minute read

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...