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DNA Reading Frame Analysis

Doug Eernisse DEernisse at fullerton.edu
Thu Nov 9 01:39:06 EST 1995


In article <rmh-0811950835330001 at async15-11.remote.ualberta.ca>,
rmh at gpu.srv.ualberta.ca (Robert Hornbeck) wrote:

>    I am in search of some software that will extract or predict the
> reading frames in a DNA sequence.  I know that DNA Strider performs this
> task but I can not afford the $200 USD for it.  I am an undergrad working
> on a little phylogenetics and it is tough predicting this sort of thing
> with out software.  If any one has any recommendations I would appreciated
> it.  I am using a Macintosh LC630 but I do have access to othe computers
> as well, although I would prefer macintosh format.  You can send your
> replies to: "rmh at gpu.srv.ualberta.ca".
> 
> Thank You For Your Time
> David Frederiksen

My HyperCard stack package can do that, although these features are
a bit buried. Get the freeware package from my home page:

http://biology.fullerton.edu/people/faculty/doug-eernisse

called "DNA Stacks"

I am in the process of replacing the interface where the translation
utilities have been, so the following instructions are subject to change:

Set HyperCard RAM partition to a quite a bit (5 MB if you have the RAM
to spare). Click on HyperCard _once_ from the Finder when it is closed
and choose "Get Info" from the File menu. Change "Preferred" to 5000 K.
Any 2.0 or greater version of HyperCard or HyperCard Player should work
but the current 2.3.x is PPC native.

Open stack "DNA Translator"

Select "Utility Card" from the "Go" menu

Select "Nucleo- to Peptides" from the "Convert" menu

When prompted you probably want the "String" format option
because you can then use it in "Aligner" stack or convert
it to various formats with "String Nucleotides..." from
the "Convert" menu.

You can examine the sequences in the three reading frames on card
fields (click where you see the results appear) as well as exporting
them to file.

If your phylogenetics involves animal mitochondrial DNA, you might
also experiment with exporting DNA and amino acid gene sequences directly
to the alignment editor. About 27 or so genomes are fully supported.
The easiest way to start is to select "Get mtDNA Sequences" from
the "Data" menu of "Aligner."

Good luck,


Doug

-- 
Doug Eernisse <DEernisse at fullerton.edu>
Dept. Biological Science MH282
California State University
Fullerton, CA 92634




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