need dna editor for unix

Dan Jacobson dan.jacobson at nitelog.com
Wed Aug 4 05:12:00 EST 1993


. at FROM   :DANJ at WELCHDEV.WELCH.JHU.EDU                                  
. at SUBJECT:Re: need dna editor for unix                                 
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From: danj at welchdev.welch.jhu.edu (Dan Jacobson)
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In article <7408 at krafla.rhi.hi.is> php at rhi.hi.is (Petur Henry Petersen) writes:
>
> Well the title says it all. I need some kind of software that runs
>under UNIX which allows me to make comparisons and translate DNA into protein.
>Just email me... ThanX
>


You might want to take a look at GDE (Genetic Data Envronment) - by
Steve Smith.  You can obtain GDE by gopher or anonymous ftp.

Gopher sites:

merlot.welch.jhu.edu, select:

-->  3.  FTP Sites, Software and Data Archives For Biology/

   -->  22. GDE (Genetic Data Environment)  (Harvard)/

megasun.BCH.UMontreal.CA, select:

 -->  5.  GDE (The Genetic Data Environment)/

Anonymous ftp:

golgi.harvard.edu in pub/GDE.


Best of luck,

Dan Jacobson

danj at welchgate.welch.jhu.edu




And from the Readme file I snagged from Tim's site:

-----------------------------------------------------------------------------

...The GDE is a set of programs for multiple sequence
alignment and analysis. The GDE currently runs on SUN SparcStations using
OpenWindows 2.0 or MIT X11R4.  The programs use an expandable user interface
which allows the addition of external analysis functions without any rewriting
of code.  Analysis functions can be written in any language ('C',Fortran,
Pascal
Basic, shell scripts), and can be seamlessly merged into the systems menu/
dialog box interface.

The system supports several data types, nucleic and amino acid sequences,
text, and masking sequence, and three forms of color highlighting.  The system
can handle enormous alignments limited only by the amount of virtual memory
on your workstation.

Sequences can be edited under several levels of protection, as well
as by aligned groups.  The system has several external analysis
functions included for such things as automated alignment, searching,
homology recognition, and phylogenetic analysis.

The programs are not in the public domain, but are and will continue to be
available for free.  Distribution includes full source code, and binaries
along with a users manual.

Steven Smith

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