Suggestion: Seq analysis control panel for Macintosh

Art Eschenlauer eschen at molbio.cbs.umn.edu
Mon Jun 28 15:41:00 EST 1993


"A Molecular Biology Control Panel"

  Here is an idea for a productivity tool for the molecular biologist. It
would be a simple sequence information processor. I'm not proficient enough
at mac programming to set it up correctly. If there's anyone out there
who is (and wants to), let me describe what it would look like. I will 
begin with the interface:

  Are you familiar with the Wordfinder Plus?It is a thesaurus that is set up 
as a control panel that you can switch on and off. When on, it puts the word 
"WF+" on the menubar, visible and usable from any application. It can see 
(and replace) any word that was selected in the application prior to WF+ 
being invoked. Such an interface would be useful to the molecular biologist, 
especially (but not exclusively) to be used in conjunction with a word 
processor. Right now I'm designing and analysing primers, and I find myself 
thinking "Now I need DNA strider to translate this sequence, I can go to 
SeqSpeak to hear it or convert it to another format (or run ReadSeq), DNaid 
is the only program on my Mac that does codon usage frequency, and Amplify 
is where I test my primers for PCR..." Most of these functions are pretty 
common, and I could really use a combination of them in one spot, so here's 
my suggestion for the "Molbio Control Panel":

  When activated, MCP would place "M" on the menubar. The user would select 
a string in any text-based application and then pull down the M menu. He 
would see the following options (possibly with reconfigurable 
keyboard shortcuts):

- speak sequence
- sequence submenu 
  - reverse
  - complement
  - reverse-complement
  - change case submenu
  - edit with a sequence editor
    I don't know of it would be better to replace the selection or to
      put the altered sequence onto the clipboard. Perhaps the user
      could choose in a preferences dialog....
- translation menu
  - check-offs for 1 letter or 3 letter translation
  - translate submenu
  - codon frequency submenu
     Both submenus would show the six reading frames as options
       and would put output onto the clipboard 
       in "UWGCG codonfrequency" format
- restriction sites
     Output positions of sites to clipboard
     Both strands scanned for assymetrical sites
- sequence format conversion via built-in ReadSeq (routines by Don Gilbert
        from ftp.bio.indiana.edu)
     Output submenu to check off output to file (via Std File dialog) 
       or clipboard (which means MCP would also have a built in pretty
       print)
     Format submenu to check off output format
- anything else you think that the molecular biologist 
     might like to have handy, like a regular expressions pattern search

  Obviously, this tool would need a preferences file!

  I suppose that other cute names for this package might be "Mole" or "Mole 
Bio" or "Gene Finder" or...

  Consider this not so much a request as a suggestion.

Art (eschen at molbio.cbs.umn.edu)




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