internet addresses for protein kinase data...

Dan Jacobson danj at welchgate.welch.jhu.edu
Fri Apr 2 09:39:09 EST 1993


In article <1pgd6p$2q5 at usenet.INS.CWRU.Edu> sxk29 at po.CWRU.Edu (Susan Kretschmer) writes:
>
>Hi!  I'm relatively new to the Internet, and I wondered if I could get
>help with specific internet addresses for sites with data on the following
>subjects:
>
>protein kinases
>retroviral insertion sequences
>oncogenes and anti-oncogenes (any available data)
>public domain software for mol bio applications (if there is any :-)
>
>I've read the FAQ, but am uncertain exactly where to get started looking
>for this stuff; I don't know much about gophers.  Can anyone tell me how
>to get started?  
>

Protein kinases:

You can obtain the db of protein kinase catalytic domains (maintained
by Anne Marie Quinn at the Salk Institute) by anonymous ftp from 
ncbi.nlm.nih.gov in the repository/kinase directory.  The database is sequence 
only and comes ready for searching in Fasta format.  The reference for 
each sequence is given in a seperate file.

Now for the rest of your questions you really should get gopher.  Once you
have gopher you can search genbank for 

retroviral and insertion

and you will come up with the following entries which you can read and 
save on your hard disk if you'd like.

      1.  GIBIL2MLA Gibbon ape MLA 144 abnormal IL-2 allele at GaLV(SF) inse...
      2.  HUMGACTA1 Human gamma-actin pseudogene, 5' end..
 -->  3.  HUMGACTA2 Human gamma-actin pseudogene with retroviral insertion s...
      4.  MUSCKIFRN Mouse cKi-ras mRNA containing Friend virus LTR sequence.
      5.  MUSCKIRAS Mouse cKi-ras gene containing Friend virus proviral prom...
      6.  MUSIE119 Mouse IE 119 sequence inserted into processed gamma-actin.
      7.  MUSIL3IAP Mouse (cell line WEHI-3B) interleukin-3 gene, 5' region ...
      8.  MUSITS Mouse (BR6) insertion target site for MMTV retrovirus..
      9.  MUSMLVHRH Mouse (hairless) DNA with an endogenous retroviral leuke...
      10. MUSMLVHRN Mouse DNA with an endogenous retroviral leukemia virus L...
      11. MUSMYBR1 Mouse rearranged mutant c-myb gene, 5' end of retroviral ...
      12. MUSMYBR2 Mouse rearranged c-myb gene, 3' end of retroviral inserti...
      13. MUSMYCK1 Mouse c-myc proto-oncogene, 5' flank, retroviral insertio...
      14. MUSMYCK2 Mouse c-myc proto-oncogene, 5' flank, retroviral insertio...
      15. MUSRSLA6 Mouse middle repetitive LTR-like DNA sequence, clone A6..
      16. MUSRSLB12 Mouse middle repetitive LTR-like DNA sequence, clone B12...
      17. MUSRSLB8 Mouse middle repetitive LTR-like DNA sequence, clone B8..
      18. MUSRSLC4 Mouse middle repetitive LTR-like DNA sequence, clone C4..
      19. S38891 F2=retroviral insertion locus [mice, Other RNA, 1915 nt].
      20. SYNSHIRVA Synthetic helper-independent retroviral vector DNA, clon...
      21. SYNSHIRVB Synthetic helper-independent retroviral vector DNA, clon...
      22. SYNSHIRVC Synthetic helper-independent retroviral vector DNA, clon...
      23. ALRGPRV1 Rous sarcoma virus (Strain B77) proviral DNA duplicated u...
      24. MLSST1 Soule murine leukemia virus (S-MuLV) proviral LTR, clone ST...
      25. MLSST4 Soule murine leukemia virus (S-MuLV) proviral LTR, clone ST...
      26. MLT Murine leukemia virus (Tikaut) proviral LTR..
      27. QULINSA Coturnix japonica insertion sequence..
      28. QULINSB Coturnix japonica insertion sequence..
      29. QULINSC Coturnix japonica insertion sequence..
      30. QULINSD Coturnix japonica insertion sequence..


Now oncogene is a pretty big topic and a simple search of genbank
for  -  oncogene - yields hundreds of entries, however a search for

anti and oncogene

yeilds the following:

 -->  1.  DRORAP1A Drosophila melanogaster Rap1 gene, complete cds..
      2.  HUMP53G Human p53 gene for transformation related protein p53 (als...
      3.  HUMPLASINS Human anti-oncogene mRNA..
      4.  HUMRBG1G Human retinoblastoma gene 5'-region fragment.




Public domain software for mol bio:

Again, gopher is a big help here - you can use ftp look through lots of sites
one by one or you can use gopher to poke through these sites in a much
more conveniant manner (and you don't have to know all the site addresses :-).

Once you get a gopher client point it at merlot.welch.jhu.edu and go into
the  

-->  2.  FTP Sites For Biology/ 

directory and you'll see links to 56 sites which have software for
biology.  The biggest sites are:

-->  24. IUBio-Software+Data (Indiana)/
-->  38. Molecular Biology Software (Finland) /
-->  22. Gene-server: Software and PIR (Houston) /
-->  12. EMBL software (Heidelberg)/

Note you can also get your kinase data via 

-->  39. NCBI Repository FTP Archive /.


Below I'm enclosing an information sheet on gopher to help get you
started.

Best of luck,

Dan Jacobson

danj at welchgate.welch.jhu.edu


------------------------------------------------------------------------

                          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.

Dan Jacobson

-----

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:

pit-manager.mit.edu:/pub/usenet/news.answers/gopher-faq

Those without FTP access should send e-mail to mail-server at rtfm.mit.edu
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?

-------------------------------------------------------------------
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 boombox.micro.umn.edu.  Look in the directory
     /pub/gopher

--------------------------------------------------------------------
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 boombox.micro.umn.edu (134.84.132.2) in the directory
     /pub/gopher.

      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
      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 Macintosh Application, "MacGopher".
        ftp.cc.utah.edu:/pub/gopher/Macintosh *

      Another Macintosh application, "GopherApp".
        ftp.bio.indiana.edu:/util/gopher/gopherapp *

      A port of the UNIX curses client for DOS with PC/TCP
        oac.hsc.uth.tmc.edu:/public/dos/misc/dosgopher.exe

      A port of the UNIX curses client for PC-NFS
     	 bcm.tmc.edu:/nfs/gopher.exe

      A beta version of the PC Gopher client for Novell's LAN Workplace
      for DOS
         lennon.itn.med.umich.edu:/dos/gopher

      A VMS DECwindows client for use with Wollongong or UCX
         job.acs.ohio-state.edu:XGOPHER_CLIENT.SHARE


     * 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:

       Type=1
       Host=boombox.micro.umn.edu
       Port=70
       Path=
       Name=Gopher Software Distribution.

 
     Or point your gopher client at boombox.micro.umn.edu, 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
     "consultant.micro.umn.edu" (134.84.132.4) 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
     ------------------------- ---------------  ------  -------------
     consultant.micro.umn.edu  134.84.132.4	gopher  North America
     gopher.uiuc.edu           128.174.33.160   gopher  North America
     panda.uiowa.edu           128.255.40.201	panda   North America
     gopher.sunet.se           192.36.125.2     gopher  Europe
     info.anu.edu.au           150.203.84.20    info    Australia
     gopher.chalmers.se        129.16.221.40    gopher  Sweden
  


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