From: POSTMASTER@GUNBRF.NBRFNET.GEORGETOWN.EDU
Newsgroups: bionet.software
Subject: Announcements of PIR Network Request Service
Date: 1 Oct 92 17:47:20 GMT
Distribution: bionet


              Announcements of the Protein Identification Resource
                            Network Request Service

Highlights
1. PIR Release 34 and NRL_3D Release 10
2. Updated Distribution Information
3. Database Standardization Efforts
4. Internet Addresses for Anonymous FTP and Network Request Service
5. FASTA Searches for NRL_3D Only
6. Network Request Service Command Summary

Announcements
1. PIR Release 34 and NRL_3D Release 10

As of 30 September Release 34 of the PIR databases and Release 10 of the
NRL_3D database (corresponding to Brookhaven Protein Data Bank Release 61)
are now available through the PIR On-line system and Network Request Server.
Distribution of the tape and CD-ROMs of the new release will begin shortly.

Database   Release Sequences  Residues
  PIR1     34.00   10,550     3,591,370   
  PIR2     34.00   16,188     4,330,190   
  PIR3     34.00   18,162     5,284,017   
  NRL_3D   10.00    1,457       244,804

Growth of the PIR databases is documented in the file DBGROWTH.LIS available
through the Network Request Server.  The following files are also available
through the Server:
  the list of superfamiles in PIR1 is in SUPERFAM.LIS,
  the list of keywords in PIR1 and PIR2 is in KEYWORDS.LIS,
  the list of features in PIR1 and PIR2 is in FEATURES.LIS.


2. Updated Distribution Information

The databases and programs of the PIR are distributed on magnetic tape and
on TK50 and TK70 cartridges in VAX/VMS format and in ASCII card image format;
the protein databases are updated and distributed on a quarterly basis, the
sequence analysis software package is updated irregularly.  The prices listed
are per release and are subject to change. Tapes may be ordered on a one-time 
or on a standing order basis.

The PIR-International Protein Sequence Database ($250) contains substantially
sequenced proteins and sequences translated from nucleic acid sequences.
The database is divided into three data sets categorized by the degree of
annotation in the sequence entries.  The sequences in the PIR1 data set (and
some of the PIR2 data set) have been annotated to identify post-translational
modifications, active sites, signal sequences, disulfide bonds, etc.  The PIR3
data set contains minimal entries that have not yet been examined by
scientific staff.  The datatape also contains the NRL_3D database of sequence
information extracted from the Brookhaven Protein Data Bank.

The VAX/VMS format of the protein sequence datatape contains the PSQ
(Protein Sequence Query) and the NAQ (Nucleic Acid Query) retrieval programs
and programs for creating user databases.  As a service to our users, the PIR
is also including files required to use the PIR database with the GCG software.

The ATLAS multidatabase retrieval program is available on CD-ROM ($100) along
with the PIR-International Protein Sequence Database, the ALN protein alignment
database, the NRL_3D database, the PATCHX database, and the GenBank Genetic
Sequence Databank.  The ATLAS program is currently  designed to run on PC/DOS
and VAX/VMS systems.  Support for UNIX and Mac will be added.

The PATCHX database ($250) is produced by MIPS at the Max Planck Institute
for Biochemistry, Martinsried, Germany.  The PATCHX database includes all
protein sequences (not identical with or contained in sequences from PIR1,
PIR2 and PIR3) from the following databases: MIPSOwn MIPS preliminary entries,
PIRMOD MIPS/PIR preliminary entries, MIPSH MIPS yeast entries, NRL_3D
Brookhaven Data Bank Sequences, MIPSTrn MIPS preliminary translations,
EMTrans (EMBL translation by F. Pfeiffer), SwissProt, GenPept (GenBank(R)
translation by Los Alamos Nat. Lab.), Kabat, and PSeqIP.  All sequences
that are IDENTICAL within or between databases are presented only ONCE.
Also sequences completely contained within others have been removed. 

The NBRF-PIR Sequence Analysis Software tape ($200) contains programs designed
to run on a VAX computer operating under VMS version 5.  All programs are
written in VAX-11 Fortran (a superset of ANSI Fortran 77), with the exception
of the Lipman-Pearson programs (FASTA, RDF), which are written in VAX-11 C. 
Included are:
  database searching programs (SEARCH, ISEARCH, FASTA);
  global similarity programs (ALIGN, IALIGN);
  local similarity programs (RELATE & DOTMATRIX);
  and prediction programs (PRPLOT & CHOFAS - from the IDEAS package). 

More information about the databases, sequence analysis programs, tapes,
on-line services, custom services or prices can be obtained by contacting:
    Kathryn  E. Sidman
    Protein Identification Resource
    National Biomedical Research Foundation
    3900 Reservoir Road, NW
    Washington, DC  20007
    Phone: (202) 687-2121 
    FAX:  (202) 687-1662
    E-mail: PIRMAIL@GUNBRF.BITNET


3. Database Standardization Efforts

The combined staffs of the PIR-International have been engaged in a vigorous
effort to standardize the keyword and features records occurring in the PIR1
and PIR2 databases.  Previous efforts to standardize the species and reference
records and the title records for enzymes had been very successful.  The
standardization effort progressed by:
(1) determining the complete variety of information that existed in those
    records,
(2) formulating rules for which forms were acceptable and which were not,
(3) imposing those rules by correcting the non-compliant entries and
    introducing additional checking procedures during the data entry process.

The success of this standardization effort for the keyword records can be
judged from these results: in Release 30 there were 1614 different keywords
with 63% of those keywords appearing in fewer than 4 entries; in Release 34
there are 1037 different keywords and 40% of those keywords appear in fewer
than 4 entries.  The following table provides a more complete breakdown.

          Frequency of Keywords

Frequency        Different Keywords
in Entries        Rel. 30  Rel. 34
     >400               7       12
  201-400              10       24
  101-200              19       42
   51-100              38       58
   26-50               61       61
   13-25              103      105
    7-12              131      135
    4-6               218      185
    2-3               395      208
     1                632      207


4. Internet Addresses for Anonymous FTP and Network Request Service

During September the PIR Network Request Service was made available through
the National Biomedical Research Foundation's Internet address.  For users
on BITNET the address remains FILESERV@GUNBRF.  For users on Internet and
other networks with gateways to Internet the preferred address is now
  FILESERV@NBRF.Georgetown.Edu.
Provided in the last part of this announcement is a synopsis of instructions
for using this database query and FASTA sequence search service.

Each PIR release and its accompanying NRL-3D release are available for
anonymous FTP from the UH Gene-Server, ftp.bchs.uh.edu, IP address 129.7.2.43.
The login is "anonymous" and the password is your e-mail address.  The files
are kept in pub/gene-server/pir/pir_relXX/{ascii,vms}. "XX" is the release
number.  All files are stored as Unix 16-bit compressed files and the file
names end in .Z (e.g. pir.1.dat.Z) as a reminder.

The "ascii" directory contains the CODATA format files, and the "vms"
directory the NBRF format files and indices in VMS format. Note that two of
the files required by GCG V.7.X are not included; those can be generated by
GCG-supplied utilities.

Uncompress utilities are available for non-Unix systems;
  the DOS archive sites have a file "cmprs430.zip";
  the Info-Mac archives have "maccompress-32.hqx";
  and various VMS archives have "lhzcomp.exe" or "decompress.exe".
The latter is also available in pub/gene-server/pir, with a sample
(but non-working) .CLD file.

Questions about the FTP server can be directed to Dan Davison, davison@uh.edu.
Our thanks to Bill Pearson and Dan Davison for their efforts in providing FTP
access to the PIR databases.


5. FASTA Searches for NRL_3D Only

Some users had suggested that they wanted to do FASTA sequence searches
only for the sequences with known 3-dimensional structures, the sequences
extracted from the Brookhaven Protein Data Bank in NRL_3D.  Normally our
FASTA searches are done against all the protein databases, PIR1, PIR2, PIR3,
the non-redundant PATCHX (described in the August announcement and in part 2
above) and NRL_3D.  Now when the command
  USE BASES NRL_3D
is used before a SEARCH command, only the NRL_3D database will be used for
the FASTA search.  Otherwise, all the protein databases will be used.

Thanks to Ada Prochnicka-Chalufour at the Pasteur Institute for her helpful
suggestion and her hospitality this spring.


6. PIR Network Request Service Command Summary

The National Biomedical Research Foundation Protein Identification Resource
network request service is a full-function fileserver and database query
system.  It has been operating since August 1990 and 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@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
  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 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
  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 for
  HELP topic
for example
  HELP SEARCH

In addition to the commands, help instructions are also available on the
following topics:
  Custom_Services
  Databases
  Gateway_Access
  Help_en_Espanol
  Help_en_francais
  IBM-VM_BITNET
  On-Line_Access
  PIR_Distribution
  VAX-VMS_BITNET

Because of network gateway communication protocols, there are limitations on
requests sent through gateways.  Users not on BITNET or INTERNET who access
BITNET 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 Dr. John S. Garavelli at POSTMASTER@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 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 FILESERVer.

The DEPOSIT and QUERY commands 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 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
Not all commands work with all databases; please read the information returned
by the command HELP DATABASES.
------------------------------------------------------------------------
                                 Dr. John S. Garavelli
                                 Database Coordinator
                                 Protein Identification Resource
                                 National Biomedical Research Foundation
                                 Washington, DC  20007
                                 POSTMASTER@GUNBRF.BITNET
                                 POSTMASTER@NBRF.Georgetown.Edu
Newsgroups: bionet.software