Announcing BMERC Gopher/WWW Servers

Bill Schmidt schmidt at darcy.bu.edu
Fri Oct 7 20:40:22 EST 1994


The BioMolecular Engineering Research Center  &  Molecular Biology
Computer Research Resource  at Boston University (collectively
referred to here as BMERC) announces the availability of its  Gopher  
and  World Wide Web (WWW)  servers.



   *  The URL for the BMERC WWW server Home Page is:

               http://bmerc-www.bu.edu/


   *  The gopher server can be accessed at the address given immediately
      below.  NOTE that the gopher can be accessed BOTH through gopher 
      and through a link provided on the BMERC WWW server Home Page.

               bmerc-gopher.bu.edu


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The BMERC research objectives are summarized immediately below, and the
tools and interfaces described below which are available through the BMERC
gopher/WWW servers either support, or result from, the Center's work.

   *  To develop statistical and other computational approaches
      which will detect syntactic and semantic patterns in DNA,
      RNA, and protein sequences.

   *  To use statistical/computational approaches to identify the
      structure, function, and regulation associated with such
      patterns.





The component tools and interfaces, described below, are in an early stage of
development.  We will continue to expand and develop these tools/interfaces
based on our own experiences with them, and by actively soliciting and 
incorporating feedback from our collaborators, user community, and beta 
test sites.



SOFTWARE DISTRIBUTION
---------------------
Through its FTP site, accessible through its gopher/WWW servers, BMERC 
distributes, free of charge as part of its dissemination program, software 
that it develops in meeting the objectives listed above, as well as 
non-commerical software developed by others, datafiles, and support 
information.  In particular, the PLSearch database of homologous protein family
patterns, and the associated search-and-discovery software, is
available.





PROTEIN STRUCTURE/HOMOLOG DATABASE
----------------------------------
The gopher/WWW servers provide access to ProLink, a locally-developed 
integrated database of protein structure, sequence homolog, and 
functional pattern information installed in a relational format under 
Sybase.  

The current data is derived from the Brookhaven Protein Data 
Bank (proteins of known structure), Protein Family Pattern Database 
(also known as the Plsearch Database), Enzyme Nomenclature Database, 
Protein Core Structures Database (currently under development here at 
BMERC), and includes homolog links to the BLOCKS database, GenPept, 
SWISS-PROT and Medline.  It also has indirect links to Prosite, OMIM
and GDB databases.

Currently, ProLink can be searched using the gopher/WWW SQL query
library, a set of prepackaged SQL queries.  In the near future, access
to ProLink will be greatly expanded by increasing the size of the SQL 
query library, and by implementing the WWW server's mosaic-based forms
interface.  In the latter approach, a user is able to specify a wide 
range of search parameters, thereby permitting the user to tailor a 
search to his/her specific interests.
 



E-MAIL SERVER
-------------
Also coming available is an email server which analyzes an input amino
acid sequence to determine the probable tertiary structural class of
the protein and the probable secondary structure for each of the
residues.  A short description of the calculations being performed, 
references, and instructions for accessing the email server are 
available through the gopher/WWW servers.



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