103. Profile Search 
Manfred D. Zorn and David Demirjian 
Lawrence Berkeley National Laboratory, Berkeley, Calfornia 
DGDemirjian@lbl.gov 

Protein Sequence & Profile Search Software Product 

The ultimate goal of this project is to produce a software product that will facilitate the ability to query many protein sequence and profile databases. Platform portability has been tested to include Solaris, Linux, and Windows 95 platforms. This software builds an optimized database from the protein and sequence database files for maximum performance. 

The current features of this software system include: 

• Prosite database search for profile and pattern matches on a given sequence query.
• Command line & Gui Interface
• Search Parameters:
• From / To Match Ratio
• Inclusive / Exclusive match ratio selection
• Cut off score maximum
• Number of acceptable matches
• Full profile documentation display
• Search results are saved to a file to interface with other products. A visual display is also presented for the gui user interface. The detail of the search results are grouped under the accession id of the matching profile and grouped by match location on the query sequence.
• Java GUI and command line interface.

• Query protein sequence databases for a given pattern. 
• Incorporate the facility to accept varied formats of the query sequence.

Interactive graphical display of search results. 

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