Announcement of PIR Server

POSTMAST at gunbrf.bitnet POSTMAST at gunbrf.bitnet
Tue Nov 27 15:56:00 EST 1990


            Announcement of the Protein Identification Resource
                     BITNET Network Request Service

The National Biomedical Research Foundation Protein Identification Resource
now 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:
  Gateway_Access
  IBM-VM_BITNET
  On-Line_Access
  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.

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.

  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.

  BASES
This command will return a list of the accessible databases and the number
of entries each contains.  Currently, this selection of databases cannot
be changed during network access.  The databases available 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
  N             NBRF Nucleic
  GB            GenBank(TM)                           as received
  EMBL          EMBL                                  as received
Access to these and additional databases can be provided to on-line users.

  DEPOSIT FORM or DEPOSIT AUTHORIN
    submission text
  END DEPOSIT
This command will allow the submission of 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.

  GET code
This command will return the full text of an entry with the code matching
the code provided.  These codes are found in the lists returned by one of
the search commands (ACCESSION, AUTHOR, JOURNAL, KEYWORD, SPECIES, or
TITLE).  The format of the code is a database abbreviation, a colon,
and four to ten alphanumeric characters.

  INDEX
This command will return a list of the files that can currently be sent
by the PIR FILESERVER using the SEND command.

  JOURNAL citation
This command will return a list of entry codes and titles for entries with
a journal citation matching the portion of the citation provided.

  KEYWORD words
This command will return a list of entry codes and titles for entries with
any keyword, or portion of a keyword, matching the words provided.  You may
provide any number of groups of three or more alphanumeric characters
expected in a single keyword entry.

  RETURN address
If you are sending mail from a non-BITNET network through a gateway, you may
need to provide a return address different from the one posted on the message
in order for your output to be sent to you correctly.   The RETURN command
will allow you to correct your return address.

  SEARCH parameters sequence
    or
  SEARCH parameters
    sequence text
  END SEARCH
This command will allow a sequence to be compared in a FASTA search
(see W.R.Pearson & D.J. Lipman PNAS (1988) 85:2444-2448) with the PIR
databases.  You may send either protein or nucleotide sequences; however,
only the PIR protein sequence databases will be searched.  Nucleotide
sequences will be translated in six reading frames according to a selectable
genetic code, and those translated protein sequences will be compared against
the PIR protein sequence databases.  The SEARCH command may be used in two
forms, either on a single line with parameters and sequence, or on multiple
lines with the parameters on the line with the SEARCH command, followed by
lines with the sequence and an END SEARCH command on the line following the
end of the sequence.  There are two optional parameters for the SEARCH command,
KTUP and NUC.  The KTUP parameter sets the ktup value for the FASTA program.
The NUC parameter specifies that the sequence is a nucleotide sequence, and
can select the genetic code to be used for the translation of that sequence.

  SEND filename
This command will instruct the FILESERVER program to send, by separate
electronic transmission, the specified file.  A list of the currently
available files can be obtained by using the INDEX command.

  SPECIES name
This command will return a list of entry codes and titles for entries with
the species matching the portion of a species name provided.  The species
name may be the Latin genus and/or species name, or a common name.  Because
the names of some viruses contain the common name of the host species,
entry codes and titles for entries with the species of viruses infecting
a species may also be listed.

  SUGGEST text
     or
  SUGGEST
    text
  END SUGGEST
This command will submit the text of your message to an NBRF staff member.
You may use it to suggest modifications or improvements to our FILESERVER
and PIR database services.  You may either place the text on the same line
with the SUGGEST command, or you may use any number of lines for the text
followed by the END SUGGEST command on the line after the last line of the
text.

  TITLE title
This command will return a list of entry codes and titles for entries with
any portion of a title matching the word provided.  You may provide any
number of groups of three or more alphanumeric characters expected in a
single title.

------------------------------------------------------------------------
                                 Dr. John S. Garavelli
                                 Database Coordinator
                                 Protein Identification Resource
                                 National Biomedical Research Foundation
                                 Washington, DC  20007
                                 POSTMASTER at GUNBRF.BITNET



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