DNA software question

Nick Theodorakis via methods%40net.bio.net (by nick.theodorakis from gmail.com)
Mon Jan 12 22:04:12 EST 2009

Han wrote:
> Colleague at Cornell Medical College has a very old Mac with an old version
> of DNAStar, which he likes very much.  His use is not very intensive, but
> primer design, sequence alignment etc are used relatively often.
> Since the Mac is about to die, he would like software for a PC (XP Pro)
> that could best perform those functions.  DNAStar (new version) costs
> $1,000/year in licensing costs, which colleague doesn't regard as a wise
> investment.  What are his best options for free or cheap software with
> similar capabilities as what he wants of DNAStar (primer design, sequence
> alignment, etc)?

For primer design, I and nearly everyone I know use Pimer3. There is a
web version:


which is also now built into the NCBI primer blast page:


Downloadable source is also available:


Nick Theodorakis
nick_theodorakis from hotmail.com
contact form:

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