Announcements of the Protein Information Resource

Wed Dec 2 11:53:52 EST 1992

               Announcements of the Protein Information Resource
                            Network Request Service

1. Submitting Sequence Data to GenBank, EMBL, DDBJ or PIR
2. PIR Network Request Service Command Summary

1. Submitting Sequence Data to GenBank, EMBL, DDBJ or PIR

The National Biomedical Research Foundation Protein Information Resource has a
Network Request Server that, among other things, accepts electronic submission
of sequence data.  Sequence data submission policies have been designed by
agreement among the nucleotide and protein sequence databanks.  We wish to take
this opportunity to restate for BIONEWS subscribers a few general guidelines on
submission of their sequence data.

Researchers should submit nucleotide sequence data directly to GenBank or EMBL
for assignment of an accession number prior to publication. Derived amino acid
sequence data may also be included at the same time.  Amino acid sequence data
submitted in this way to GenBank, EMBL or DDBJ are eventually passed on to PIR,
and need not be submitted separately to PIR.  This is done so correct cross-
references can be made between nucleotide and protein sequence accession

All other amino acid sequences may be submitted directly to PIR when the
authors permit their public release prior to publication.  Sequences submitted 
for publication in the journal Protein Science are automatically passed on to
the PIR for assignment of accession numbers prior to publication, and those
authors do not need not to make separate submissions.

Authors are strongly urged to use the sequence submission software package
AUTHORIN to submit their sequence data to the databanks; a free copy (for
either the IBM PC or Macintosh) can be obtained by sending your request and
regular postal mailing address to:
  authorin at net.bio.net

Japanese authors who use the NEC 9801 PC should communicate directly with
DDBJ, as these machines use a version of DOS that is significantly different
enough to render the discs unreadable on MS-DOS computers here. The staff at
DDBJ will forward the data to the appropriate databank via electronic mail.
DDBJ may be contacted at:
  ddbjsubs at flat.nig.ac.jp

The address for GenBank submissions is:
  GenBank Submissions
  Mail Stop K710
  Los Alamos National Laboratory
  Los Alamos, NM  87545
  Telephone: (505) 665-2177
  Electronic mail:  gb-sub at life.lanl.gov

The address for EMBL submissions is:
  EMBL Data Submissions
  Postfach 10.2209
  D-6900, Heidelburg
  Federal Republic of Germany
  Telephone (+49) 6221-387-258
  Electronic mail: DATASUBS at EMBL-Heidelberg.DE

The address for DDBJ submissions is:
  DNA Database of Japan
  Center for Genetic Information Research
  National Institute of Genetics
  111 Yata
  Mishima, Shizuoka 411
  Telephone (+81) 559-75-3651
  Electronic mail:  ddbjsubs at flat.nig.ac.jp

The address for PIR submissions is:
  PIR Submissions
  National Biomedical Research Foundation
  3900 Reservoir Road, NW
  Washington, DC  20007
  Telephone: (202) 687-2121
  Electronic mail:  FILESERV at GUNBRF.BITNET, FILESERV at NBRF.Georgetown.EDU

While we would again urge that AUTHORIN be used as the first choice in data
submission tools, the GenBank/EMBL/PIR Data Submission Form can be obtained
either by sending a message consisting of the word DATASUB to
  retrieve at net.bio.net
or by sending a message consisting of the words
to the FILESERV address.  This form can be filled in using any text editor,
saved in ASCII (text) format, and mailed electronically or on disk to the

Please, do not submit data either by electronic mail or on disk in files that
are formatted for word processing programs.  Such files are almost always
unreadable except by systems with the same configuration of computer, operating
system and word-processing program.  For files sent by disk, either DOS or Mac
formatted disks can be used but we would prefer receiving regular "double
density" disks rather than "high density" disks.

Additional information about submitting sequence data to PIR can be obtained
by sending the message HELP DEPOSIT to the FILESERV address.

2. PIR Network Request Service Command Summary

The National Biomedical Research Foundation Protein Information Resource
network request service is a full-function fileserver and database query
system.  Operating since August 1990 it 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 or FILESERV at NBRF.Georgetown.EDU on Internet.
The server recognizes the following commands sent either in a mail message,
or (if the sender is on BITNET) in a command message or 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 nucleic 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 matching sequences 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, dates or formats 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 form
  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 the
server 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
John S. Garavelli (POSTMAST at GUNBRF on BITNET, POSTMASTER at NBRF.Georgetown.EDU on
Internet).  We will confirm a return address for you and may instruct you to
use the RETURN command to ensure 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
nonstandard 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 server.

The DEPOSIT and QUERY commands, and the SEARCH and SUGGEST commands (in their
multiline form) must be followed by their respective END commands after the
text appearing on the 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.

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 monthly
  PIR3          PIR Unverified Entries                weekly
  ALN           PIR Alignment Entries                 semiannually
  NRL_3D        Brookhaven Data Bank Sequences        quarterly
  PATCHX        MIPS PIR-Supplementary Database       quarterly
  N             NBRF Nucleic
  GB            GenBank (TM)                          as received
  GBSUP         GenBank (TM)                          as received
  GBNEW         GenBank (TM) New Entries              weekly
  EMBL          EMBL                                  as received
  EMBLSUP       EMBL                                  as received
In the FASTA output of the SEARCH command the abbreviation for PATCHX is
shortened to PATX and NRL_3D is shortened to NR3D; the longer abbreviation
should be used to retrieve an entry with the GET command.  Not all commands
work with all databases; please read the information returned by the command
                                 Dr. John S. Garavelli
                                 Database Coordinator
                                 Protein Information Resource
                                 National Biomedical Research Foundation
                                 Washington, DC  20007
                                 POSTMASTER at GUNBRF.BITNET
                                 POSTMASTER at NBRF.Georgetown.Edu

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