The best DNA analysis software?

Marc Champagne M.Champagne at -nospam-cellbio.duke.edu
Tue Jul 15 05:12:10 EST 1997


In article <dchong-ya023480001207971922490001 at oitnews.harvard.edu>,
dchong at gonzo.tch.harvard.edu (Jayhong A Chong) wrote:

> I am currently using Geneworks on the Mac and this is pretty satisfactory,
> but I was wondering what other people have tried and liked.  I generally do
> restriction analysis, multiple sequence alignments, primer design, and
> sequencing projects.  I have used PCgene and GCG, and I have access to Mac,
> Intel based PC, and SGI platforms.
> 
> Thanks for you input.

DNAstar
-------

We (a couple labs in our dept) have been using the DNAstar package.  It does
the job, but is not intuitive.  A lot of features don't work (set defaults)
and many tools are cumbersome for Mac users.  One nice thing is that it's
a package of many little software, so you don't have to launch a huge software
for minor things.

I've personally found 8 bugs, including one that ended up giving the wrong amino
acid for a given codon.  The company has been fixing these, but in some cases
they didn't understand the science behind the bugs.

GeneInspector/GeneConstruction kit
----------------------------------

I've also tried a demo of GeneInspector and GeneConstruction kit (from Textco,
www.textco.com) and i think it's awesome.  It was written by a molecular 
biologist/Mac user, which is one of the best recipe to make a great application.
I was truly amazed at the cloning features.  The software lets you try to clone
by copy/paste your restriction fragments into a vectors site, and if you screw
up it'll tell you you can't do it, and suggest blunting.  Once you have the new
construct, you can ask to see what any restriction digest would look like on
a gel, even partial digests.  That's only the beginning...  

I wish we could buy it, but since we already have somehting that works, why 
pay for something else?  The only thing i couldn't find in the Textco 
applications were a sequence editor/aligner (to make contigs).

Definitely try the demo...

m.champagne at cellbio.duke.edu

-- 
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