3.3.1. About

BLAST, or Basic Local Alignment Search Tool, is a collection of tools that are used to search for and find regions of local similarity between sequences. The program compares nucleotide or protein sequences to sequence databases, and calculates the statistical significance of the matches. This software suite has been released free to the public by the National Centre for Biotechnology Information.

3.3.2. Usage

BLAST can be used for protein-protein comparisons or nucleotide-nucleotide comparisons. Before an example of the usage is presented, we must first define some environmental variables.

BLAST requires the presence of 2 datasets. One dataset is the input sequence that you want to search for, and the other dataset is the database that you want to search against.

Use the following procedure to run blast

3.3.3. Running Blast with SGE

This section gives a very simple example of running BLAST through the provided batch system SGE.

3.3.4. Further Information

For further information about BLAST and its usage, please refer to the following sources