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.eduPIRMAIL 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.BITNETPOSTMASTER at NBRF.Georgetown.Edu
