[Zbrafish] Software for DNA/Protein analysis

Chi-Bin Chien via zbrafish%40net.bio.net (by chi-bin.chien from neuro.utah.edu)
Tue Oct 19 15:07:08 EST 2010

Hi Becky,

I very much like ApE (A plasmid Editor), which is freeware from Wayne  
Davis in Erik Jorgensen's lab:
It runs on Windows or Mac, and is excellent for designing subcloning  
strategies. It is very good showing useful restriction sites, and can  
calculate Gateway reactions (even 3- or 4-insert LR reactions). It can  
import Genbank-format files with features; lets you specify features  
by hand; can automatically recognize features based on a template  
file; and draws nice graphical maps.

There are some alignment tools that I haven't learned to use. Doesn't  
do things like ClustalW alignments.
Still, it does nearly all of my day-to-day molecular biology work, and  
you can't beat the price.


On Oct 16, 2010, at 2:21 PM, Burdine, Rebecca D wrote:

> Hi everyone,
> I am looking to replace our DNA/Protein analysis software and  
> wondered if anyone had a recommendation for a product that they  
> liked.  I have a very old version of DNAStar that we like but isn’t  
> compatible with Windows 7. It is pretty expensive to replace so I  
> want to check other options.
> We need something pretty simple that will let us make DNA sequence  
> files, protein sequence files, maps of features like restriction  
> enzyme sites or domain regions, sequence alignment, etc.
> Any suggestions?
> Becky
> ---------------------------------------------------
> Rebecca D. Burdine, Ph.D.
> Assistant Professor
> Dept. of Molecular Biology
> Princeton University
> Washington Road Mof 433
> Princeton, NJ 08544
> Phone: (609) 258-7515
> Fax: (609) 258-6730
> Email: rburdine from princeton.edu
> Admin Assistant: Anna Schmedel (609) 258-5028
> <ATT00001..txt>

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