Announcements of the Protein Information Resource
PIR-International
20 June 1997
Update on PIR Services on the World Wide Web
The latest improvements in the Protein Information Resource (PIR) World Wide
Web search and retrieval services provide full access to the current version
of PIR-International Protein Sequence Databases and provide links to other
genome, sequence and structure databases.
Starting from the PIR homepage http://www-nbrf.georgetown.edu/pir/ you can
locate information on:
* Descriptions of PIR products and services
* Searching and retrieving from PIR databases
* Getting PIR databases by anonymous FTP at NBRF.Georgetown.EDU
and other locations
* PIR database current release information
* How to link to the PIR databases on the Web
The PIR databases currently accessible at the PIR Web site are:
* The PIR-International Protein Sequence Database containing naturally
occurring, wild-type proteins uniquely organized by homology and
taxonomy, and updated weekly. The current version includes
PIR1 Classified and Annotated Entries 13706 entries 5125282 residues
PIR2 Annotated Entries 77276 24432811
PIR3 Unverified Entries 3830 867477
PIR4 Unencoded or Untranslated Entries 238 43412
---- --------------------------------- ----- --------
PIR total for the four sections 95050 30468982
* NRL_3D sequence--structure database of sequence information extracted
from the Brookhaven Protein Data Bank. The current version corresponds
to PDB Release 79 thru May 1997, with 10717 entries 1897913 residues
* ALN database of sequence alignments for protein families, superfamilies
and homology domains with 2853 entries
Starting from the PIR Web search and retrieval facility
http://www-nbrf.georgetown.edu/pir/searchdb.html
these services are available for the PIR Protein Sequence Database:
* The entry request service http://www-nbrf.georgetown.edu/nbrf/get.html
retrieves entries based on entry code, PIR reference, PIR accession or
cross-reference identifiers for other databases.
* The text request service http://www-nbrf.georgetown.edu/pir/find.html
provides both basic and advanced search forms to retrieve entries
using Boolean operations for substrings in title, species, author,
publication, keyword, superfamily, feature and genetics fields.
* The selection list service http://www-nbrf.georgetown.edu/nbrf/lists.html
retrieves based on alphabetized lists of species, keywords,
superfamilies, genes and publication journal abbreviations.
* The sequence search service http://www-nbrf.georgetown.edu/nbrf/scan.html
scans the PIR-International Protein Sequence Database for exact sequence
matches.
These Web services are available separately for the NRL_3D database:
* The entry request service http://www-nbrf.georgetown.edu/nbrf/getnrl.html
includes retrieval by PDB code.
* The text request service http://www-nbrf.georgetown.edu/nbrf/findnrl.html
provides a search form to retrieve entries by substrings in title,
species, author, publication, keyword, and feature fields.
* The sequence search sevice http://www-nbrf.georgetown.edu/nbrf/scannrl.html
scans the NRL_3D Sequence Database for exact sequence matches.
For the ALN Alignment Database, the entry request service
http://www-nbrf.georgetown.edu/nbrf/getaln.html
provides entry retrieval by either entry code or title search.
With a retrieved entry, other options are available.
* Retrieved entries can be displayed in user selectable formats.
* Other related entries can be retrieved based on species, keywords, or
superfamily.
* Related alignments can be retrieved, or links can be followed to alignment
and classification information at MIPS or the University of Texas.
* The sequence shown in the entry can be sent to BLAST or PSORT servers.
Also, a sequence can be constructed that corresponds to a source sequence
from which the entry was prepared or to a domain or product feature.
The constructed sequence can be edited before it is submitted to BLAST
or PSORT servers.
* Hyperlinks can be followed to other databases such as the Brookhaven
Protein Data Bank, EMBL (at EBI), GenBank, GenPept (at NCBI), the
Human Genome Data Base, MedLine (through PubMed), and TIGR.
The PIR Web site provides information and methods that enable outside databases
like the Human Genome Data Base to hyperlink to the databases at the PIR.
You may also want to visit the Web site of MIPS, our collaborators in Germany
http://www.mips.biochem.mpg.de/
Munich Information Center for Protein Sequences
Max Planck Institute for Biochemistry
Am Klopferspitz 18a
Martinsried 82152 GERMANY
Please note that other Web sites and data depositories do not always have the
latest quarterly release of the PIR-International Protein Sequence Databases
that are available from the NBRF or MIPS. You should check our homepages for
the current weekly version or quarterly release information and then go to the
most convenient FTP or WEB site that has that current release or version.
The PIR Web Site was developed by Dr. Bruce C. Orcutt, Dr. Leslie M. Arminski
and Kathryn E. Sidman of the National Biomedical Research Foundation.
Correspondence regarding the Web site should be directed to:
Dr. Bruce C. Orcutt
Protein Information Resource
National Biomedical Research Foundation
3900 Reservoir Road, NW
Washington, DC 20007 USA
Phone: 202-687-2121
Fax: 2025-687-1662
E-mail: PIRMAIL at NBRF.Georgetown.EDU
PIR is a registered mark of NBRF
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Dr. John S. Garavelli
Associate Director
Protein Information Resource
National Biomedical Research Foundation
Washington, DC 20007
POSTMASTER at NBRF.GEORGETOWN.EDU
