This tutorial will explain how to use GSAT to compare two sequences and retrieve a Standard Score in standard deviations. GSAT is newer replacement for the deprecated GAP program.

GSAT  Stands for Global Sequence Alignment Tool. This program will allow you to preform a pairwise alignment based on a default of (500) shuffles. This tool is designed for finding homology between two distantly related proteins.

AverageQuality= MeanNWScores +/- StandardDeviation.
The“ Z” Value, or “ Standard Score” is then calculated as follows:

To use GSAT, go to terminal and type


Alternatively, a web based version of GSAT may be found on our BioTools webpage.

Typically, the default settings for GSAT are sufficient. (shuffles = 100, gap open penalty =  8, gap extend penalty = 2,  scoring matrix = BLOSUM62)

Once you submit your request, scroll to the very bottom of your terminal or browser. The result you are looking for is called:

“Standard Score”

Anything with a Standard Score (Z-Score) of 10 standard deviations or greater is significant (Doolittle, 1980)


Please cite:

GSAT (V.S. Reddy, M.Saier, 2010)