Algorithm is a computable set of steps arranged thus in order to achieve a certain end. There are various algorithms used in bioinformatics and not all are necessarily deterministic. Some are in fact known as randomized algorithms that incorporate randomness.
Classification of algorithms in Bioinformatics
Classification by purpose
Each algorithm has a goal. The Quick Sort algorithm for instance sorts data in ascending or descending order, but algorithms in bioinformatics are grouped by their particular purpose.
Classification by implementation
An algorithm has different fundamental principles:
It goes in a loop. Usually used for functional programming, it uses repetitive constructs and is best used for problems such as the towers of Hanoi problem which is imbued with recursive implementation and therefore has these iterative equivalents. An example is the following retrieved from Horton (2004):
Table 3: Pseudo code for "naive" pattern matching algorithm.
character[] pattern, text;
integer i, j;
for (i=0;i
