Remote Sequence Comparison

POSTMAST at NBRF.BITNET POSTMAST at NBRF.BITNET
Thu Nov 7 16:33:00 EST 1991


            Announcement of the Protein Identification Resource
                     BITNET Network Request Service

Five commands and access to two new sequence databases have been added to the
network request service.  The new commands are FEATURE, HOST, QUIT, SUPERFAMILY
and TAXONOMY.  They are described below in more detail.  The two new databases
are NRL_3D which contains the sequence information extracted from the
Brookhaven Protein Data Bank, and GBNEW which contains the weekly update
sequences from GenBank (TM).  These databases are automatically available
through all the commands that can use them.

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
  FEATURE        list entry codes and titles by feature table entry
  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
  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

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
  NRL_3D        Brookhaven Data Bank Sequences        quarterly
  N             NBRF Nucleic
  GB            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.

  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.

  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.  A list of the features currently in the database
can be obtained by the command SEND FEATURES.

  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, FEATURE, HOST, KEYWORD, SPECIES,
SUPERFAMILY or TITLE).  The format of the code is a database abbreviation, a
colon, and four to ten alphanumeric characters.

  HOST host-name
This command will return a list of entry codes and titles for entries in the
PIR databases only with a host name 



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