[Zbrafish] Re: DNA/Protein analysis

Adam Miller via zbrafish%40net.bio.net (by amiller from fhcrc.org)
Tue Oct 19 12:24:30 EST 2010

Hi Becky,

I'm a fan of Geneious (http://www.geneious.com/) because it is very  
easy to use, has a nice graphical interface that makes sequencing very  
easy, good RE tools, cloning, makes nice graphics, and does all the  
simple stuff that I need. It is not as good as Sequencher for  
alignments (in Geneious you have to fiddle a bit more) but it is not  
horrible either. They have a free trial at the above website so you  
can try it out.

Also, you might check out ApE (http://biologylabs.utah.edu/jorgensen/wayned/ape/ 
) (http://ape-a-plasmid-editor.wikispaces.com/) which I have not used  
much, but I have had it recommended to me. Its free and was developed  
in the Jorgensen lab at Utah by Wayne Davis. I think it only does DNA/ 

good luck,

On Oct 19, 2010, at 10:03 AM, zbrafish-request from oat.bio.indiana.edu  

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>   1. Software for DNA/Protein analysis (Burdine, Rebecca D)
> From: "Burdine, Rebecca D" <rburdine from Princeton.EDU>
> Date: October 16, 2010 1:21:45 PM PDT
> To: "zbrafish from oat.bio.indiana.edu" <zbrafish from oat.bio.indiana.edu>
> Subject: [Zbrafish] Software for DNA/Protein analysis
> 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
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   Adam C. Miller
   Division of Basic Sciences
   Fred Hutchinson Cancer Research Center
   1100 Fairview Ave. N, Mail Stop B2-152
   Seattle, WA 98109-1024
   tel: 206.667.5697

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