PIR Protein Database Network Server

POSTMAST at gunbrf.bitnet POSTMAST at gunbrf.bitnet
Thu May 23 10:14:00 EST 1991


                  The Protein Identification Resource
                     BITNET Network Request Service

The National Biomedical Research Foundation Protein Identification Resource
has a full-function network fileserver and database query system.  This
automatic network server is capable of handling database queries, sequence
searches and sequence submissions, in addition to fileserver requests.  To
use this server, request commands should be directed to FILESERV at GUNBRF on
BITNET.  The FILESERVER recognizes the following commands sent either in a
mail message, or (if the sender is on BITNET) in command messages or in a file:

  Command        Action
  -------        -----------------------------------------------
  ACCESSION      list entry codes and titles by accession number
  AUTHOR         list entry codes and titles by author
  BASES          list accessible databases
  DEPOSIT        deposit entry for database submission
    END DEPOSIT  terminate deposit entry
  GET            return entry by entry code
  HELP           return HELP instructions
  INDEX          list SENDable files
  JOURNAL        list entry codes and titles by journal citation
  KEYWORD        list entry codes and titles by keyword
  RETURN         change return address for gateway mail
  SEARCH         search for sequence by FASTA procedure
    END SEARCH   terminate sequence for searching
  SEND           send file
  SPECIES        list entry codes and titles by species
  SUGGEST        leave suggestion for PIR staff
    END SUGGEST  terminate suggestion text
  TITLE          list entry codes and titles by title

Multiple commands can be sent with one command on each line of a mail message
or file.  Commands should not be sent on the Subject line of a mail message.
Receipt of command messages and files will be acknowledged immediately.  Mail
messages will be acknowledged by return mail.

For help in using any of the commands, send a request of the form
  HELP topic
for example
  HELP SEARCH

In addition to the commands, help instructions are also available on the
following topics:
  Custom_Services
  Gateway_Access
  IBM-VM_BITNET
  On-Line_Access
  PIR_Distribution
  VAX-VMS_BITNET

Because of inter-network gateway communication protocols, there are limitations
on requests sent through gateways.  Users not on BITNET or INTERNET who will be
accessing BITNET through inter-network gateways should read and carefully
follow these instructions before sending requests.  Only mail message requests
(not command messages or files) can be sent through gateways.  Because the
addresses posted on gateway mail do not always work for the return, before you
send requests through inter-network gateways it is strongly recommended that
you first contact Dr. John S. Garavelli at POSTMASTER at GUNBRF on BITNET.  We
will confirm a return address for you and may instruct you to use the RETURN
command to insure that your request output will reach you.  It is not necessary
to do this if you are on BITNET or INTERNET.

The DEPOSIT command must, and the SEARCH and SUGGEST commands may, be followed
by their respective END commands when text appears on intervening lines.  The
DEPOSIT command requires, and the SEARCH command optionally uses, parameters
that appear on the same line as the command.  Because of the complexity of
these commands, users should obtain and carefully read the help instructions on
these commands before attempting to use them.

To address John Warren's question, the TITLE command can be used particularly
effectively because the PIR entry titles include with the protein name such
information as the species and the Enzyme Commission number.
------------------------------------------------------------------------
                                 Dr. John S. Garavelli
                                 Database Coordinator
                                 Protein Identification Resource
                                 National Biomedical Research Foundation
                                 Washington, DC  20007
                                 POSTMASTER at GUNBRF.BITNET



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