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
