----------------------------------------------------------------------------- ************************* * How to obtain PROSITE * ************************* Name : PROSITE.GET Topic : Describes how you can obtain a copy of PROSITE or browse through the database using various network information retrival tools Last revised: March, 1995. ----------------------------------------------------------------------------- Scientific enquiries concerning PROSITE can be sent to: Amos Bairoch Medical Biochemistry Department CMU University of Geneva 1, Rue Michel Servet 1211 Geneva 4 Switzerland Email : bairoch@cmu.unige.ch Tel : +(41-22) 784 40 82 Fax : +(41-22) 347 33 34 ----------------------------------------------------------------------------- ** Release history *** Previous release : 12.1 of October 1994 Current release : 12.2 of March 1995 Next release : 13.0 of June 1995 ----------------------------------------------------------------------------- ** The PROSITE files *** PROSITE .DOC: PROSITE documentation file PROSITE .DAT: PROSITE data file PROSITE .LIS: List of documentation entries PROSITE .GET: How to obtain PROSITE (this document) PROSITE .PRG: List of programs that make use of PROSITE PAUTINDX.TXT: Authors index PROSUSER.TXT: User Manual for PROSITE PROFILE .TXT: Syntax for the profiles in PROSITE EXPERTS .TXT: List of on-line experts for PROSITE and SWISS-PROT ----------------------------------------------------------------------------- --- How to obtain PROSITE --------------------------------------------------- ----------------------------------------------------------------------------- 1) You can subscribe from the EBI EMBL Data Library to receive four times per year a set of three CD-ROM disks which, among other things, contain SWISS-PROT, PROSITE and ENZYME. To subscribe or for further enquiries contact: Email: datalib@ebi.ac.uk Tel : +44-1223-494 400 Fax : +44-1223-494 468 ----------------------------------------------------------------------------- 2) You can get it on CD-ROM along with many other data bases from the National Center for Biotechnology Information (NCBI). That particular CD-ROM name is "NCBI Data Repository". For information on how to subscribe to receive this CD-ROM, contact: NCBI - Data Repository National Library of Medicine NIH / Bldg. 38A 8600 Rockville Pike Bethesda, MD 20894 USA Email: info@ncbi.nlm.nih.gov Tel : +301-496 2475 Fax : +301-480 9241 ----------------------------------------------------------------------------- 3) If you have access to a computer that is linked to Internet, you can obtain (for free) PROSITE from the following FTP servers: Organism : ExPASy (Geneva University Expert Protein Analysis System) Address : expasy.hcuge.ch (or 129.195.254.61) Login : User=Anonymous Password=Your name or email address Directory: /databases/prosite Organism : National Center for Biotechnology Information (NCBI) Address : ncbi.nlm.nih.gov (or 130.14.20.1) Login : User=Anonymous Password=Your name or email address Directory: /repository/prosite Organism : EBI Address : ftp.ebi.ac.uk (or 193.62.196.6) Login : User=Anonymous Password=Your name or email address Directory: /pub/databases/prosite Organism : National Institute of Genetics (Japan) ftp server Address : ftp.nig.ac.jp (or 133.39.16.66) Login : User=Anonymous Password=Your name or email address Directory: /pub/db/prosite This is by far the best way to get PROSITE. Its fast, free, and easy to do ! ----------------------------------------------------------------------------- 4) If you have access to a computer which can send electronic mail, you can get PROSITE by electronic mail from the EBI file server. To do so, you must send a message to the following address: netserv@ebi.ac.uk Your message should contain the following lines: get PROSITE:PROSITE.DAT get PROSITE:PROSITE.DOC get PROSITE:PROSITE.LIS get PROSITE:PAUTINDX.TXT get PROSITE:PROSUSER.TXT get PROSITE:PROFILE.TXT get PROSITE:PROSITE.GET get PROSITE:PROSITE.PRG You will then get back (a few hours or a few day laters depending on your node location and on the trafic) the PROSITE files by electronic mail. But the Server automatically breaks down data files into 100 Kb chunks, this means that you will receive some files splits into different parts and that you must "glue" them together with a text editor. ----------------------------------------------------------------------------- 5) PROSITE is available from the ExPASy WWW server The World-Wide Web (WWW), which originated at CERN, is a powerful global information system merging networked information retrieval and hypertext. It gives access, using hypertext links, to the documents and information contained in all the existing WWW servers around the world, as well as to the data obtainable through other information retrieval systems like WAIS, Gopher, X500, etc. To access a WWW server, one has to run on a local computer a client program (a WWW browser), which displays hypertext documents. The ExPASy WWW server allows access, using the user-friendly hypertext model, to the SWISS-PROT, PROSITE, ENZYME, SWISS-2DPAGE and SWISS- 3DIMAGE databases. Using the various links implemented in these databases, it is possible to navigate between them as well as to access other databases such as EMBL/GenBank, REBASE, FlyBase, MaizeDB, Lista, SubtiList, PDB, HSSP, GCRDb, OMIM and Medline. A WWW server can be accessed on the internet through its Uniform Resource Locator (URL), the addressing system defined by the WWW model. The URL for the ExPASy molecular biology WWW server is: http://expasy.hcuge.ch/ or http://129.195.254.61/ To access a WWW server, you need to run a browser (or client) program on your local computer. Browsers exist for a variety of machines and may be obtained by anonymous ftp. ExPASy can be used with any WWW browser, but we recommend either NCSA Mosaic or Netscape Navigator. Both are very flexible and powerful browsers with a graphical user interface; they are available for Unix boxes using X11/Motif; for Apple McIntoshes and for Microsoft Windows. You can get them from various FTP sites, for example: ftp.ncsa.uiuc.edu (for Mosaic) ftp1.netscape.com (for Netscape) For more information on the ExPASy WWW server, you can read the following article: Appel R.D., Bairoch A., Hochstrasser D.F. A new generation of information retrieval tools for biologists: the example of the ExPASy WWW server. Trends Biochem. Sci. 19:258-260(1994). ----------------------------------------------------------------------------- 6) PROSITE is available as a source on WAIS (Wide Area Information Server). WAIS is a set of products supplied by different vendors to help end- users find and retrieve information that is stored as "sources" on computer networks. To use PROSITE with WAIS you need to include the prosite.src file in your in your wais-sources directory. Individual PROSITE entries comprising patterns and documentation may be separately retrieved using WAIS software. WAIS software and a comprehensive list of sources including prosite.src may be obtained by anonymous FTP from Thinking Machines Corporation (think.com or 131.239.2.1) in the directory /wais. Dr. Tin-Wee Tan from the Department of Biochemistry of the National University of Singapore (NUS) (email: bchtantw@nuscc.nus.sg) and Dr. Derek Kiong of the Department of Information Systems and Computer Science (email: isckbk@nuscc.nus.sg) have kindly made PROSITE available on WAIS. ----------------------------------------------------------------------------- 7) If you have a Gopher client installed on your system then you can search in the PROSITE documentation or pattern files with key words. At least two Gopher hosts provide this service, one at the Indiana University in Bloomington; maintained by Don Gilbert (gilbert@bio.indiana.edu), and the other at the Swiss EMBNet node at the Basel Biozentrum; maintained by Reinhard Doelz (doelz@urz.unibas.ch). The link to add to your Gopher server the Indiana host is: Name=IUBio Biology Archive, Indiana University (experimental) Port=70 Type=1 Path= Host=ftp.bio.indiana.edu The link for the Basel Biozentrum host is: Name=bioftp EMBnet Switzerland (experimental) Port=70 Type=1 Path= Host=bioftp.unibas.ch ----------------------------------------------------------------------------- 8) PROSITE is also redistributed by many commercial companies along with their sequence analysis software (for example: by IntelliGenetics on CD- ROM with PC/Gene, or IG-Suite, by GCG on tape, by DNA*, etc.) -End-of-document-------------------------------------------------------------