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PIR Network Request Service

Wed Jul 1 12:53:00 EST 1992

            Announcement of the Protein Identification Resource
                        Network Request Service

Two commands and access to one new database have been added to the PIR network
request service.  The new commands, CROSS and GENE, are described below in more
detail.  For reasons of program access, the GenBank database is broken into
three components, GB, GBSUP and GBNEW.  The GBNEW database contains the
GenBank weekly update entries.  GBSUP contains regular GenBank entries in
a supplemental database (presently these are the GenBank Primate entries)
and GB contains all the other regular GenBank entries.  All these GenBank
databases are automatically available through all the commands that can use
them.  Particular databases may be selected with the USE BASES command, and
the command
will select all the GenBank databases, and only those databases, for
subsequent database query and retrieval commands.

The National Biomedical Research Foundation Protein Identification Resource
network request service is a full-function fileserver and database query
system.  It has been operating since August 1990 and is capable of handling
database queries, sequence searches and sequence submissions, in addition to
fileserver requests.  To use this server, request commands should be sent 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
  AND            combine QUERY commands with Boolean AND
  AUTHOR         list entry codes and titles by author
  BASES          list accessible databases
  CROSS          list PIR entry codes and titles corresponding to
                 a particular nucleotide sequence database entry
  DEPOSIT        deposit entry for database submission
    END DEPOSIT  terminate deposit entry
  FEATURE        list entry codes and titles by feature table entry
  GENE           list entry codes and titles for a gene name
  GET            return entry by entry code
  HELP           return HELP instructions
  HOST           list entry codes and titles by host species
  INDEX          list SENDable files
  JOURNAL        list entry codes and titles by journal citation
  KEYWORD        list entry codes and titles by keyword
  MEMBER         list alignments containing entry code as a member
  NOT            combine QUERY commands with Boolean NOT
  OR             combine QUERY commands with Boolean OR
  QUERY          begin collecting QUERY commands
    END QUERY    terminate collecting commands and execute QUERY
  QUIT           ignore the remaining text (E-mail signature blocks)
  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 or correction for PIR staff
    END SUGGEST  terminate suggestion text
  SUPERFAMILY    list entry codes and titles by superfamily name
  TAXONOMY       report taxonomy for scientific or common name
  TITLE          list entry codes and titles by title
  USE            set databases or dates to use in limited searches

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 for
  HELP topic
for example

In addition to the commands, help instructions are also available on the
following topics:

Because of network gateway communication protocols, there are limitations
on requests sent through gateways.  Users not on BITNET or INTERNET who
access BITNET through local or 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 addresses posted on gateway mail do not always work for the return,
before you send requests through 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
usually necessary to do this if you are on BITNET or INTERNET, unless your
system employs a local remailer or your mail program applies a non-standard
return address (for example a personal name on the FROM: line).

The BITNET network and the network gateways impose strict limits on file size.
Poorly posed database queries may result in output so extensive that it could
not be returned by network mail.  Therefore, an output limit of 1000 lines for
each command and 3000 lines for each request is imposed by the PIR FILESERVer.

The DEPOSIT and QUERY commands 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 these four
commands are so complex, users should obtain and carefully read the help
instructions before attempting to use them.

Here is a brief synopsis of each server command.

  ACCESSION number
This command will return a list of entry codes and titles for entries with
accession numbers matching the left portion of the accession number provided.

This command performs a Boolean AND operation in a QUERY, using the set of
entries collected by the preceding commands and selecting those that
additionally meet the condition specified in the next command.

  AUTHOR name
This command will return a list of entry codes and titles for entries with an
author matching the portion of the author name provided.

This command will return a list of the accessible databases and the number of
entries each contains.  The databases available through the PIR Network Server
and their abbreviations for code specification are as follows:
  Abbreviation  Database                              Update Schedule
  PIR1          PIR Annotated and Classified Entries  quarterly
  PIR2          PIR Preliminary Entries               approximately bimonthly
  PIR3          PIR Unverified Entries                weekly
  ALN           PIR Alignment Entries                 quarterly
  NRL_3D        Brookhaven Data Bank Sequences        quarterly
  N             NBRF Nucleic
  GB            GenBank (TM)                          as received
  GBSUP         GenBank (TM)                          as received
  GBNEW         GenBank (TM) New Entries              weekly
  EMBL          EMBL                                  as received
Access to these and additional databases can be provided to on-line users.

  CROSS number
Use this command to find PIR entries that are the translation products of
nucleotide sequence database entries.  This command will return a list of
entry codes and titles for entries in the PIR databases only with a
cross-reference to the accession number provided in one of the nucleotide
sequence databases.

    submission text
This command will allow the submission of protein sequence entries prepared in
a standard format.  The PIR accepts submissions in the electronic version of
the GenBank/EMBL/PIR Data Submission Form, or in the Transaction Protocol
Format of the GenBank AUTHORIN program.  This command MUST be followed on the
same line by either FORM or AUTHORIN to indicate the type of deposit, and by
the END DEPOSIT command at the end of the text of the entry.  Only one DEPOSIT
command should be sent with each request.  A separate form must be submitted
for each sequence.  Forms with more than one sequence and requests with more
than one DEPOSIT command cannot be accepted.
It is important that nucleotide sequences including authors' protein sequence
translations be submitted to only to GenBank or EMBL, as appropriate, and not
to the PIR FILESERVer.  GenBank and EMBL forward protein sequences to the PIR
International with no further effort required on the part of the author.

  FEATURE feature-name
This command will return a list of entry codes and titles for entries in the
PIR databases only with an entry in the feature table matching the portion of
the feature name provided.  

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