Update on PIR Services on the World Wide Web

POSTMASTER at NBRF.Georgetown.Edu POSTMASTER at NBRF.Georgetown.Edu
Fri Jun 20 12:39:17 EST 1997


               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
------------------------------------------------------------------------
                                 Dr. John S. Garavelli
                                 Associate Director
                                 Protein Information Resource
                                 National Biomedical Research Foundation
                                 Washington, DC  20007
                                 POSTMASTER at NBRF.GEORGETOWN.EDU




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