A brief introduction to SSEARCH
SSEARCH performs a rigorous Smith-Waterman alignment between a protein sequence and a protein database, or with DNA sequence to another DNA database (not available in NPS@).

Availability in NPS@
SSEARCH is available :

So, for example, you can use SSEARCH to find similar sequences in a database built from an ACNUC query or after a PATTINPROT search.

SSEARCH parameters are not currently available for the user.
By default the number of description and the number of alignment are set to 500.
The expected threshold is set to 10.0.
The comparison matrix is BLOSUM50.
The gap opening penalty is -12 and gap extending penalty is -2.
To retrieve these informations see the line "Information and statistics : [SSEARCH]" in NPS@ SSEARCH result file.

NPS@ SSEARCH output example
The NPS@ SSEARCH output is divided into three parts.