Announcements of PIR-International

POSTMASTER at NBRF.GEORGETOWN.EDU POSTMASTER at NBRF.GEORGETOWN.EDU
Fri Jul 29 17:38:48 EST 1994


   Announcements of the Protein Information Resource PIR-International


Highlights
1. Summaries for PIR-International Release 41.00 and Associated Data Sets
2. Summary of Database Developments in Release 41.00
3. PIR Network Request Service


Announcements
1. Summaries for PIR-International Release 41.00 and Associated Data Sets

Release 41.00 of the PIR-International database and Release 15.00 of the
NRL_3D database (corresponding to Brookhaven Protein Data Bank Release 65) are
now available through the PIR On-line system and the PIR Network Request
Server. The PIR1, PIR2, PIR3, NRL_3D databases are distributed on tape, and
those databases plus PATCHX, ECOLI, ALN and Complex Carbohydrate Structure
Database (CCSD) are distributed on the Atlas of Protein and Genomic Sequences
CD-ROM.

Database   Release Entries    Residues
PIR1       41.00   12,404     4,529,307   Classified and Annotated Sequences
PIR2       41.00   35,689     9,933,981   Annotated Sequences
PIR3       41.00   22,755     6,352,981   Unverified Sequences
NRL_3D     15.00    3,911       679,392   Protein Sequences in Brookhaven PDB
PATCHX     41.00   31,883     7,547,908   Protein Sequences
ECOLI       2.2       557     2,676,167   Genomic Sequences
ALN         5.1     1,133                 Multiple Protein Sequence Alignments

The ATLAS CD-ROM also includes the Complex Carbohydrate Structure Database
(Release 9) with its access program CarbBank Version 2.6 for PC- or MS-DOS,
IBM-compatible microcomputers. The ATLAS CD-ROM includes documentation, an
Installation Manual and Tutorial for CarbBank.  The ATLAS program, which
accesses all of the other data sets on the CD-ROM, does not access the Complex
Carbohydrate Structure Database.

The NRL_3D Database, produced by the PIR since 1989, is a protein sequence
database extracted from the Brookhaven Protein Data Bank (PDB) coordinate data
files; it provides an interface between the Protein Sequence Database and the
PDB and provides access to the PDB data via computerized sequence searching
and comparison methods.  The MIPS PATCHX data set used in conjunction with the
Protein Sequence Database provides the most complete collection of protein
sequence data currently available in the public domain.  The ALN database
provides a set of multiple sequence alignments of related protein sequences
from the PIR-International Protein Sequence Database.  The ECOLI database
contains genomic sequences from Escherichia coli K12.

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:
  PADD.LIS      PIR1 entries added since Release 40.00
  PREV.LIS      PIR1 entries with revised sequences since Release 40.00
  SPECIES.LIS   species count for PIR entries
  SUPERFAM.LIS  superfamiles recorded in PIR1 and PIR2
  KEYWORDS.LIS  keywords employed in PIR1 and PIR2
  FEATURES.LIS  features cataloged in PIR1 and PIR2
  JOURNALS.LIS  recognized journal abbreviations
  ALNBASE.LIS   a description of the ALN database
  ALNTITLE.LIS  titles in the ALN database
  NRLTITLE.LIS  titles in the NRL_3D Database
To obtain these and other files from the PIR Network Request Server, follow the
instructions in the last section of these announcements.

Orders for the ATLAS CD-ROM are accepted, WITHOUT PREPAYMENT on institutional 
purchase orders, by FAX or E-mail.  For further information in the US and the
Americas, please contact:
                Kathryn Sidman, Technical Services Coordinator
                      Protein Information Resource (PIR)
                National Biomedical Research Foundation (NBRF)
                           3900 Reservoir Rd., NW
                              Washington DC 20007
                             FAX: (202) 687-1662
                            phone: (202) 687-2121
                     E-mail: PIRMAIL at nbrf.georgetown.edu
                             PIRMAIL at gunbrf.bitnet

In Europe contact:
              Martinsried Institute for Protein Sequences (MIPS)
                    Max-Planck-Institute for Biochemistry
                          8033 Martinsried, Germany
                             FAX:  49 89 8578 2655
                            phone: 49 89 8578 2657
                   E-mail: mewes at ehpmic.mips.biochem.mpg.de

In Asia and Oceania contact:
           Japan International Protein Information Database (JIPID)
                         Science University of Tokyo
                        2669 Yamazaki, Noda 278 Japan
                             FAX:  81 47 122 1544 
                            phone: 81 48 124 1501
                       E-mail: Tsugita at JPNSUT31.BITNET

For information about CarbBank contact:
         Dana Smith
         CarbBank/CCSD Manager
         114 W. Magnolia St.
         Suite 305
         Bellingham, WA  98225
         Phone:     (206) 733-7183
         FAX:       (206) 733-7283
         EMail:     Internet: 76424.1122 at Compuserve.Com


2. Summary of Database Developments in Release 41.00

All of the features in the PIR-International Protein Sequence database
designated as "Active site", "Binding site", "Cleavage site", "Cross-link",
"Disulfide bonds", "Inhibitory site", or "Modified site" now carry one of these
four status indicators, "experimental", "predicted", "atypical", or "absent". 
With these status indicators on the features, researchers can quickly test
whether a particular sequence pattern accurately predicts a feature showing
correct positives (those with "experimental"), as well as false positives
(those with "absent") and false negatives (those with "atypical") depending on
the particular hypothesis.  Prior to the use by PIR of the "absent" status, the
experimental determination of a feature being absent could not be distinguished
from the case of missing data.  


3. PIR Network Request Service

The National Biomedical Research Foundation Protein Information Resource
Network Request Server 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.

The databases available through the PIR Network Server and their abbreviations
for code specification are:
  Abbreviation  Database                              Update Schedule
  PIR1          PIR Classified and Annotated Entries  weekly
  PIR2          PIR Annotated Entries                 weekly
  PIR3          PIR Unverified Entries                weekly
  ALN           PIR Alignment Entries                 quarterly
  NRL_3D        Brookhaven Data Bank Sequences        as received
  PATCHX        MIPS PIR-Supplementary Database       quarterly
  N             NBRF Nucleic
  GB*           GenBank (TM)                          as received
  GBNEW         GenBank (TM) New Entries              weekly

To use this server, request commands should be sent to
  FILESERV at GUNBRF on BITNET or
  FILESERV at NBRF.Georgetown.EDU on Internet.

To obtain a description of the Network Request Server, instructions for its
use, and a summary of commands, one of the following commands
  Help
  Help_en_Espanol
  Help_en_francais
should be sent in the body of the mail message. (Commands should NOT be sent
on the Subject line of a mail message.)

To obtain one of the files mentioned in section 1, send the command
  SEND file_name

Multiple commands can be sent with one command on each line of a mail message
or file.   Receipt of BITNET command messages and files will be acknowledged
immediately. Mail messages will be acknowledged by return mail.

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).

------------------------------------------------------------------------
                                 Dr. John S. Garavelli
                                 Database Coordinator
                                 Protein Information Resource
                                 National Biomedical Research Foundation
                                 Washington, DC  20007
                                 POSTMAST at GUNBRF.BITNET
                                 POSTMASTER at NBRF.Georgetown.Edu



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