Good primer design software for mac??

Mark Siddall mes at zoo.toronto.edu
Wed Jun 22 21:56:14 EST 1994

In article <djackson-220694121345 at> djackson at welchlink.welch.jhu.edu (Donald Jackson) writes:
>Does anyone have any recommendations for a good mac based PCR primer design

YES.  GeneJockeyII.  (I should start getting paid by the distributors,
as this is the 3rd time, i think, that I've expounded on the virtues
of this software... and no, I don't have stock in the company).

>program?  I'd like to find a program that will:
>-check for other possible "mispriming" sites in a template with primers
>I've designed

Absolutely.  In fact, I just did this today!! For a potential probe, though
the principles are identical.

Here's what you do...
... create a GJII sequence file (you can cut-and-paste from any other
   word-processor document and then click on clean-up or from sequences
   downloaded from genbank or even type it in raw).

... with that GJII sequence file open, click on "find" and drag over to 
   "in sequence"

... this brings up a box in which you can type in your desired sequence.
    Then click on "find mismatches".

... this will find the site in the sequence with the least mismatched 
    bases, and will highlight it in the sequence window and tell you
    the number of mismatches required to make it fit.

... to find other sites of varying mis-match go back up and instead of
    "find" click on "find again"

>-let me specify one primer, then come up with another one to go with it at
>some specified distance range

Well, not precisely, but you could make it do it.  There is an option
that will let you find priming sites.  You may specify the length of
the primer and the GC/AT ratio (even a range) and it will discover in the open 
sequence window appropriate priming sites automatically avoiding internal
complementarity and 3'/5' complementarities.

>-predict extinction coefficients (i.e., e260's)

Dunno.  Wouldn't be surprised though.

>and just otherwise do more than what's included in MacVector.
>I'll post a summary of replies.  

Do so.


Yer welcome.


Mark E. Siddall                "I don't mind a parasite...
mes at vims.edu                    I object to a cut-rate one" 
Virginia Inst. Marine Sci.                     - Rick
Gloucester Point, VA, 23062

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