MPSRCH email server in Bergen, Norway

Linda Akselberg linda at lind.ii.uib.no
Thu Jan 18 09:12:15 EST 1996


An experimental email server for biological sequence database searches is now 
available at the Department of Informatics, University of Bergen, Norway, at 
the adress:

                           mpsrch at ii.uib.no

through the collaboration of the Biocomputing Research Unit, University of
Edinburgh, the Department of Informatics, University of Bergen and the
Norwegian EMBnet node in Oslo.

This server gives you access to MPSRCH Version 2.1A, a suite of database 
search programs for the massively parallel MasPar computer, to aid the rapid
identification of novel biological sequence and functional relationships
for new sequences. The programs were written by J.F.Collins in the University 
of Edinburgh, UK, and, when run on the Bergen MasPar's 16384 processors, are 
the world's fastest implementations of these exhaustive search programs.

MPSRCH uses the Smith-Waterman local similarity algorithm, and performs
an exhaustive search of the whole database against the whole of the
query sequence.

MPSRCH can be used for both protein as well as nucleic acid searches,
backtranslated protein query against nucleic acids database, and nucleic
acids query against backtranslated protein database. 
The programs we are offering for the time being are:

MPsrch_pp    -   protein query against protein database
MPsrch_ppa   -   protein query against protein database, affine gap costs
MPsrch_nn    -   nucelic acids query against nucelic acids database
MPsrch_nna   -   nucelic acids query against nucelic acids database, 
                     affine gap costs

The programs offer a wide variety of parameters to control the search.
All of these have sensible default values, set in an intelligent manner
based on long term experience. Therefore, all the user is required to
specify for an initial search is the name of the program, and the query 
sequence. All parameter settings, either defaults or user-specified, 
are reported back to the user to provide an idea of the nature of the
search, and what else might be done.

The databases that are currently available are Swissprot (protein database)
and EMBL (nucleic acids database), and we always keep the most recent 
releases. The daily updates of EMBL and the weekly updates of Swissprot
are available as well.

There is also an extensive help information system to support the users
of this email server. For a start, send a message containing only the
word "help" to obtain general information about the mpsrch service.

For support and advice from a human being, contact mpsrch-support at ii.uib.no.

This service is running on a computer dedicated to research activities,
and might on rare occasions be more heavily loaded than desirable. In
such cases, please have patience. The service is experimental in that it 
is now on trial and will be evaluated after some time.

Linda Akselberg                 John F. Collins
Dept. of Informatics            Biocomputing Research Unit,
University of Bergen            Edinburgh University,
Norway                          Scotland, UK.
email: linda at ii.uib.no          jfc at biocomp.ed.ac.uk
phone: +47 55 54 40 36          +44 131 650 5365 if outside UK.
                                  0 131 650 5365 in UK.

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