Network Protein Sequence Analysis (NPSA, NPS@) image
This site is a fork of the original PRABI NPS@ server


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May 17th, 2024: NPS@ updated (see NEWS).


SSEARCH help

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 :

Parameters
Some parameters are currently not 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.

References


Last modification time : Mon Dec 5 15:48:28 2022. Current time : Sun May 19 10:42:19 2024. User : public@44.221.70.232.

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