Reposting of PIR FILESERVER Announcement

POSTMAST at gunbrf.bitnet POSTMAST at gunbrf.bitnet
Sat Mar 30 11:43:00 EST 1991


            Announcement of 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, operating since August 1990, 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 local or 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 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 inter-network gateways impose strict file size
limits.  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 total for each request is imposed by the
PIR FILESERVer.

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 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 appropiate, 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.

  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 in the IUPAC
standard single letter code; 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 nucleotid



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