Exons:
Relevant bits of information for using the MUSC Shared Resource,
 the BioMolecular Computing Resource (BCR).

Exon_65 EMBOSS version 2.6.0 at MUSC.
EMBOSS--European Molecular Biology Open Software Suite
 


1) Running the EMBOSS programs at MUSC will require that you add a line to your
   ".cshrc" file. That line should read:

  source /usr/common/bcr/EMBOSS/startup.csh

   Save the modified file and log out and login again OR
   type "source .cshrc" to activate the changes.

   An alternative would be to remember to execute the source command
   manually each time you want to work with the EMBOSS programs.

2) Here's a link to a listing of the EMBOSS programs along with what analyses they perform.
    EMBOSS

3) At the command line, you can type

   wossname -help 
 
   To launch a program which scans the program headings for keywords.

4) The EMBOSS programs may be executed by typing the program name on a UNIX command line
   (after you have performed step one above) for example

    antigenic oohu.pir1
 
    EMBOSS programs can read GCG formatted files.
    For programs like antigenic there is only text output and any terminal emulator program
    will be suitable for such programs. However, a number of the EMBOSS programs produce
    graphics output. For these programs your best bet is to connect to a BCR server through
    the console of a workstation or via x-server software such as eXceed, MACx, eXodus or
    MIx. The graphics are then rapidly displayed in an X11 window.
  
5) The EMBOSS programs may also be executed from within the W2H interface. Click on the
Start W2H-EMBOSS  button in the popup window
and proceed. 
     
 

The BCR at the Medical University of South Carolina
URL: http://bcr.musc.edu/
Last modified: March 6, 2003- ESH

e-mail to Starr comments about this page.