how do we access protein database?

Dan Jacobson danj at
Thu Jul 22 10:25:47 EST 1993

In article <1993Jul22.085449.15024 at> wiens at writes:
>Anyone please,
>We would like to compare 6 decapeptide sequences to which we have antibodies,
>to known protein amino acid sequences from a data base, but we haven't done it
>before and don't know how to access a database such as Protein Data Base or
>Gopher.  Could someone help?  We are on a pc hooked up to a university VAX and
>are used to using internet.
>Thanks,  Darrell and Jacqui

For a similarity search of your decapeptides against the databases you'll
want to use one of the mail servers.  The instructions for these servers
are a bit long so I'll e-mail them to you seperately from this post.
Gopher is also a must for biology now - I'll include some information below
to help get you started.

Best of luck,

Dan Jacobson

danj at


                          Gopher Info

This is a heavily edited version of the Gopher FAQ intended to
give people just starting with gopher enough information to get a
client and jump into Gopher-space - a complete version can be obtained
as described below.  Once you have a gopher client point it at and welcome to gopher-space!

Dan Jacobson

danj at


Common Questions and Answers about the Internet Gopher, a
client/server protocol for making a world wide information service,
with many implementations.  Posted to comp.infosystems.gopher, 
comp.answers, and news.answers every two weeks.

The most recent version of this FAQ can be gotten through gopher, or
via anonymous ftp:

Those without FTP access should send e-mail to mail-server at
with "send usenet/news.answers/finding-sources" in the body to find out
how to do FTP by e-mail.

List of questions in the Gopher FAQ:

Q0:  What is Gopher?
Q1:  Where can I get Gopher software?
Q2:  What do I need to access Gopher?
Q3:  Where are there publicly available logins for Gopher?
Q4:  Who Develops Gopher Software?
Q5:  What is the relationship between Gopher and (WAIS, WWW, ftp)?
Q6:  Are papers or articles describing Gopher available?
Q7:  What is veronica?
Q8:  How do I connect to a specific gopher server?
Q9:  What is Available for Biology?
Q0:  What is Gopher?

A0:  The Internet Gopher client/server provides a distributed
     information delivery system around which a world/campus-wide
     information system (CWIS) can readily be constructed.   While
     providing a delivery vehicle for local information,  Gopher
     facilitates access to other Gopher and information servers
     throughout the world. 

Q1:  Where can I get Gopher software?

A1:  via anonymous ftp to  Look in the directory

Q2:  What do I need to access Gopher?

A2:  You will need a gopher "client" program that runs on your local PC
     or workstation

     There are clients for the following systems.  The directory
     following the name is the location of the client on the anonymous
     ftp site ( in the directory

      Unix Curses & Emacs   :  /pub/gopher/Unix/gopher1.12.tar.Z
      Xwindows (athena)     :  /pub/gopher/Unix/xgopher1.2.tar.Z
      Xwindows (Motif)      :  /pub/gopher/Unix/moog
      Xwindows (Xview)      :  /pub/gopher/Unix/xvgopher
      Macintosh Hypercard   :  /pub/gopher/Macintosh-TurboGopher/old-versions *
      Macintosh Application :  /pub/gopher/Macintosh-TurboGopher *
      DOS w/Clarkson Driver :  /pub/gopher/PC_client/
      NeXTstep              :  /pub/gopher/NeXT/
      VM/CMS                :  /pub/gopher/Rice_CMS/ or /pub/gopher/VieGOPHER/
      VMS                   :  /pub/gopher/VMS/
      OS/2 2.0	            :  /pub/gopher/os2/
      MVS/XA                :  /pub/gopher/mvs/

     Many other clients and servers have been developed by others, the
     following is an attempt at a comprehensive list.  

      A Microsoft Windows Winsock client "The Gopher Book"

      A Macintosh Application, "MacGopher". *

      Another Macintosh application, "GopherApp". *

      A port of the UNIX curses client for DOS with PC/TCP

      A port of the UNIX curses client for PC-NFS

      A beta version of the PC Gopher client for Novell's LAN Workplace
      for DOS

      A VMS DECwindows client for use with Wollongong or UCX

     * Note: these Macintosh clients require MacTCP.

     Most of the above clients can also be fetched via a gopher client
     itself.  Put the following on a gopher server:

       Name=Gopher Software Distribution.

     Or point your gopher client at, port 70 and
     look in the gopher directory.

     There are also a number of public telnet login sites available.
     The University of Minnesota operates one on the machine
     "" ( See Q3 for more
     information about this.  It is recommended that you run the client
     software instead of logging into the public telnet login sites.  A
     client uses the custom features of the local machine (mouse,
     scroll bars, etc.)  A local client is also faster.

Q3:  Where are there publicly available logins (ie places to telnet to
     in order to get a taste of gopher) for Gopher?

A3:  Here is a short list, use the site closest to you to minimize
     network lag.

     Telnet Public Logins:

     Hostname                  IP#              Login   Area
     ------------------------- ---------------  ------  -------------	    gopher  North America    gopher  North America 	panda   North America      gopher  Europe    gopher  Sweden  gopher  Norway     info    Australia        gopher  South America		      gopher  Ecuador        gopher  Japan

     It is recommended that you run the client software instead of
     logging into the public login sites.  A client uses the
     custom features of the local machine (mouse, scroll bars, etc.)
     and gives faster response.  Furthermore many of the basic features
     of clients - saving a file to your hard drive, printing a file
     to a local printer, viewing images, retrieving files from ftp
     sites etc.... are not available by the telnet logins.

Q4:  Who Develops Gopher Software?

A4:  Gopher was originally developed in April 1991 by the University
     of Minnesota Microcomputer, Workstation, Networks Center to help
     our campus find answers to their computer questions.  

     It has since grown into a full-fledged World Wide Information
     System used by a large number of sites in the world.

     Many people have contributed to the project, too numerous to

     The people behind the much of the gopher software can be reached
     via e-mail at gopher at, or via paper mail:
      Internet Gopher Developers
      100 Union St. SE #190
      Minneapolis, MN 55455  USA

     Or via FAX at:
      +1 (612) 625-6817

Q5: What is the relationship between Gopher and (WAIS, WWW, ftp)?

A5: Gopher is intimately intertwined with these two other systems.
     As shipped the Unix gopher server has the capability to: 
       - Search local WAIS indices.
       - Query remote WAIS servers and funnel the results to gopher
       - Query remote ftp sites and funnel the results to gopher
       - Be queried by WWW (World Wide Web) clients (either using
         built in gopher querying or using native http querying.

Q6: Are papers or articles describing Gopher available?

A6: Gopher has a whole chapter devoted to it in :

     _The_Whole_Internet_, Ed Kroll, O'Reilly, 1992 (Editors note:
                             ..Great book, go out and buy a bunch!)

     _The_Internet_Passport: NorthWestNet's Guide to Our World Online"
     By Jonathan Kochmer and NorthWestNet. Published by NorthWestNet,
     Bellevue, WA. 1993. 516 pp. ISBN 0-9635281-0-6. 
     Contact info: passport at, or (206) 562-3000

     _A_Students_Guide_to_UNIX by Harley Hahn. (publisher McGraw Hill,
     Inc.; 1993 ISBN 0-07-025511-3)

     Other references include:

     _The_Internet_Gopher_, "ConneXions", July 1992, Interop.

     _Exploring_Internet_GopherSpace_ "The Internet Society News", v1n2 1992, 

     (You can subscribe to the Internet Society News by sending e-mail to
      isoc at

     _The_Internet_Gopher_Protocol_, Proceedings of the Twenty-Third
          IETF, CNRI, Section 5.3

     _Internet_Gopher_, Proceedings of Canadian Networking '92

     _The_Internet_Gopher_, INTERNET: Getting Started, SRI
          International, Section 10.5.5

     _Tools_help_Internet_users_discover_on-line_treasures, Computerworld,
          July 20, 1992

     _TCP/IP_Network_Administration_, O'Reilly.

      Balakrishan, B. (Oct 1992)
        "SPIGopher: Making SPIRES databases accessible through the
      Gopher protocol".  SPIRES Fall '92 Workshop, Chapel Hill, North

      Tomer, C.  Information Technology Standards for Libraries,
      _Journal of the American Society for Information Science_,
      43(8):566-570, Sept 1992.

Q7: What is veronica?

A7: veronica:  Very Easy Rodent-Oriented Net-wide Index to 
     Computerized Archives.

     veronica offers a keyword search of most gopher-server menu titles
     in the entire gopher web.  As archie is to ftp archives, veronica 
     is to gopherspace.  A veronica search produces a menu of gopher
     items, each of which is a direct pointer to a gopher data source.
     Because veronica is accessed through a gopher client, it is easy
     to use, and gives access to all types of data supported by the
     gopher protocol.

     To try veronica, select it from the "Other Gophers" menu on 
     Minnesota's gopher server, or point your gopher at:

     Name=veronica (search menu items in most of GopherSpace) 


Q8:  How do I connect to a specific gopher server?

A8:  Almost all clients have the ability to connect directly to a specific
     gopher hole.  I'll use my server as an example here.

If your using a Unix gopher client you would just type:


If your using a VMS gopher client you would just type:

gopher 70

If you're using the X-windows client you would type:


If you're using Turbogopher - go into the FILE pulldown menu
and select "Another Gopher" - a box will pop up asking for the
server name - type :

If you're using the DOS Client (PCgopher III) - Select the Configure
pull down menu and choose "Application" and then fill in the
box for ...

Home Gopher Server:   

then go to the FILE pull down menu and select New Gopher.

If you still need to go through the geographical hierarchy the path is
as follows:

 -->  8.  North America/

   -->  3.  USA/

     -->  21. maryland/

       -->  1.  Computational Biology (Johns Hopkins University)/


Q9: What is Available for Biology?

A9: There is an incredible amount of software, data and information
    availble to biologists now by gopher.

Here is a brief list of the Biological Databases that you can search 
via gopher:

      1.  Search BOING (Bio Oriented INternet Gophers) <?> - Lets you search
               through all the titles of items in Bio-Gophers around the
               world and access the items returned directly.
      2.  BDT Tropical Data Base Searches/
      3.  Biotechnet Buyers Guide - Online Catalogues for Biology <TEL>
      4.  Search Protein Data Bank Headers <?>
      5.  Chlamydomonas Genetics Center /
      6.  Crystallization database/
      7.  HGMP Databases - Probes and Primers /
      8.  Museum of Paleontology TYPE Specimen Index <?>
      9.  MycDB - Mycobacterium DataBase <?>
      10. Search (Drosophila) Flybase (Indiana)/
      11. Search (GenBank + SWISS-PROT + PIR + PDB)  <?>
      12. Search AAtDB -  An Arabidopsis thaliana Database <?>
      13. Search ACEDB - A Caenorhabditis elegans Database <?>
      14. Search CompoundKB - A Metabolic Compound Database <?>
      15. Search Databases at Welchlab (Vectors, Promoters, NRL-3D, EST, OMI../
      16. Search EMBL <?>
      17. Search GenBank <?>
      18. Search Genbank - 2 <?>
      19. Search Genbank Updates <?>
      20. Search LiMB <?>
      21. Search PIR  <?>
      22. Search PIR (keyword,species...) <?>
      23. Search PROSITE <?>
      24. Search Rebase - Restriction Enzyme Database <?>
      25. Search SWISS-PROT <?>
      26. Search TFD <?>
      27. Search the C. elegans Strain List  <?>
      28. Search the DNA Database of Japan <?>
      29. Search the EC Enzyme Database  <?>
      30. Search the GrainGenes database  <?>
      31. Search the Maize Database /
      32.  Cloning Vectors: plasmids, phage, etc. <?>
      33.  EPD - Eukaryotic Promoter Database <?>
      34.  EST - Expressed Sequence Tag Database - Human <?>
      35.  wEST - Expressed Sequence Tag Database - C. elegans <?>
      36.  Kabat Database of Proteins of Immunological Interest <?>
      37.  NRL_3D Protein Sequence-Structure Database <?>
      38.  OMIM - Online Mendelian Inheritance in Man <?>
      39.  Seqanalref - Sequence Analysis Bibliographic Reference Data Ban.. <?>
      40. Search Rebase - Restriction Enzyme Database <?>
      41. Search the EC Enzyme Database <?>
      42. Search The Rodent Section of Genbank <?>
      43. Database Taxonomy (Genbank, Swiss-Prot ...)/
      44. Retrieve Full PDB Entries by Accession Number <?>
      45. Search for All Researchers funded by NIH <?>
      46. Search for Genome Researchers funded by DOE <?>
      47. Search for Researchers funded by NSF <?>
      48. Search for Researchers funded by the USDA <?>
      49. E-mail Addresses of Crystallographers/
      50. E-mail Addresses of Yeast Reasearchers/
      51. Phonebooks Around the World/
      52.  Search and Retrieve Software for All Computers/
      53.  Search and Retrieve Macintosh Software/
      54.  Search and Retrieve DOS Software/
      55.  Search and Retrieve GNU Software/
      56.  Search and Retrieve Software for Biology/
      57.  Search for Agricultural Software/
      58.  Search and Retrieve Graphics Software and Data/
      59.  Search and Retrieve all Online Perl Scripts/
      60.  FTP Sites For Biology (57 archives for software and data)/
      61.  Search the Genome Data Base (GDB)/

And the list goes on - this is just the beginning


Bonus info:

Commands for the Unix and telnet clients:

<Return> or <Right> View current item.
0-9              Move to a line #.
k or Up-arrow    Move pointer up.
j or Down-arrow  Move pointer down.
u <Left>         Go up a level.
m                Go to the first screen.
q                Exit Internet Gopher.
>                Next Page
<                Previous Page
=                Display Technical information about current item.
o                change options
?                This help screen.
A and a          Save a bookmark
s                Copy an item to a file
v                View Bookmarks
/word            Search for a word in a menu or document

Each object can be identified by its "extension"

/                Item is a directory.
.                Item is a text file.
<?>              Item is a search index.
<CSO>            Item is a CSO phone book.
<TEL>            Item is a telnet session.
<)               Item is a sound (looks like a speaker)


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