DNA software question

Aawara Chowdhury via methods%40net.bio.net (by aawara from pontiff-playground.org)
Tue Jan 13 09:33:13 EST 2009


In <Xns9B91D7F826D69ikkezelf from 216.151.153.22>,
 Han <nobody from nospam.not> wrote:

> 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)?
>

We use "ApE" (A Plasmid Editor) and "Serial Cloner".

ApE is available from:
<http://www.biology.utah.edu/jorgensen/wayned/ape/>

Serial Cloner is available from:
<http://serialbasics.free.fr/Serial_Cloner.html>

Both are free, although a donation is suggested for Serial Cloner.

ApE reads ABI sequencing trace files, does restriction digests,
sequence alignments, finds primers, finds silent restriction endonuclease
recognition sites, does translations, produces excellent annotated
plasmid maps, and can BLAST sequences.

Serial Cloner does everything that ApE does, and in addition, shRNA
design, Gateway(tm) cloning design, and one can setup ligations of
1, 2, or 3 fragments.  The plasmid maps generated by Serial Cloner are
similar to those made by DNA Strider (i.e. restriction sites but not
annotated).

AC
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