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Scan for sequence pattern (PROSITE)

The "Import" utility of SPDBV allows you to connect directly to a spdbv-server, thereby providing direct access to databases and powerfull computing facilities. Before using this service, you have to fill the "Network preferences" correctly. The following SPDBV-servers are curretly available:

 

The amino acid sequence of the current layer can be searched for the occurence of specific sequence pattern, e.g. glycosylation sites etc. Use the "Find Sequence" menu to input a search pattern. The search string can be a PROSITE pattern.

It is possible to scan the current layer sequence against all prosite pattern. This routine uses the current parameters (e.g. max. number of mismathces) as specifies in the "Find Sequence" menu.
The current prosite pattern file prosite.dat can be downloaded from

http://www.expasy.ch/prosite/

Copy this file into your "spdbv/usrstuff" directory, then use the "Search for prosite pattern" function in the "Edit" menu.

The results window allows you to highlight the different pattern in the structure (by clicking on the pattern description, e.g. "THIONIN") or to download the pattern definition from the server (by clicking on the Pattern Code e.g. "PS00271").