IUBio

Setting up a DNA analysis workstation

Alan Williams Alan at Avocado.UCR.edu
Thu May 20 00:29:55 EST 1999


Hi,

I have been running Linux as my primary OS for about 4 yrs.  I have a
strong computer science background, but am a molecular biologist by
training.  Recently we got a Pentium II 400 in the lab which I setup
a linux partition on (~8gig).  It is running KDE 1.1 with the KDM 
login manager (so everything is GUI to the non computer types in the
lab).  I have also setup the KDE mime types to atomatically recognize
certain extensions and run the appropriate molecular biology program.
The use of the system is fine for newbies, but setup and administration
are going to require mucking around on the command line.  I can't 
comment specifically on primer design, but here are some of the apps
we use:

GDE (The Fristensky lab has some nice gde menues available at 
     http://home.cc.umanitoba.ca/~psgendb/index.html#SOFTWARE)
ClustalX (Great GUI alignment program)
ClustalW
Alscript (For generating publication quality alignments)
DBWatcher (For automatic periodic blast searches, remote or local)
tacg (Great Program for digest maps)
readseq and seqio for sequence file format conversion

Here is an "ls" of my bio directory to give you a hint at what is out there:

Install              dotplot2ps           predator-2.1.2
Patterns-1.0.3       etc                  primer-3.0.3
alscript-2.04        fsap-4.0             procheck-3.4.4 bin                  
gde-2.2              readseq-930201       boxplot97_only_mesa  
gde-2.2-old          saps-sspa-04111996   boxshade-3.3.1       
lib                  seqio-1.2.2          cleanup-1.8.3        
man                  seqsee-1.3
clustalw-1.7         misc                 shadybox-2.0.3
clustalx-1.65b       naview               tacg-2.35
codontree-1.2        ncbi                 tnimage-2.8.1b
dbwatcher-2.01       ncbi-6.0             treetool-2.0.2
dna-gui-2.0          njplot               viennaRNA-1.2.1
dna-tools-1998       phylip-3.5           xylem.1.8.3

On the Non Bio side of software:

Netscape (free)
Star Office (free, can read MS Office 97 stuff)
WordPerfect 8.0 (free)
Acrobat

[ Free may mean for non-commercial use only. ]

If setup right, a linux system can provide you with a great stable 
multiuser research workstation; but it is going to take you a log more 
time to setup than a MSWindows computer.  

I should note that there are several efforts out there to build 
free newbie friendly analysis tools. Seqpup, JaMBW, Loci, and 
my own GST. JaMBW and Seqpup would be the most mature whereas Loci and GST
are pre pre alpha (ie no usable code yet).

-Alan

Linux and Bio Relevent Links:

SAL.KachinaTech.Com/Z/2/index.shtml
liposome.genebee.msu.su
http://evolution.bmc.uu.se/~thomas/mol_linux/index.html 
http://zifi.genetics.utah.edu/~zinc/linux/linux-apps.html 
http://alt-www.uia.ac.be/u/pvosta/pcrbioc.html 
http://www.gdb.org/Dan/softsearch/softsearch.html


Other Relevent Links:

home.cc.umanitoba.ca/~frist/ (Fristensky Lab)
golgi.harvard.edu/gibert-bi.html (Gilbert Lab)
barton.ebi.ac.uk or geoff.biop.ox.ac.uk
www.genetics.wustl.edu/eddy/software/
www.embl-heidelberg.de/~toldo/JaMBW.html
ftp://area.ba.cnr.it/pub/software/
ftp://ftp.bio.indiana.edu/



Jil Tardiff <jtardiff at westnet.com> wrote:
: The sorts of analyses we need to do are mostly centered around primer
: design (this is the *big* issue), restriction maps,  protein/nucleotide
: alignment and sequence editing.

: So, my question is this: do you folks think it is worthwhile to add a
: Linux partition to the lab machine and just use Linux for our DNA
: analysis needs?  I know that a number of packages exist for Linux,  but
: if any end-users could tell me about their experiences and suggestions
: for the most user-friendly programs, I would greatly appreciate it.  My
: student is a complete Linux/UNIX newbie, so I would like to make this as
: straightforward as possible for her. I'm also intrigued by GDE, but
: setting it up seems a bit formidable.

************************************************************************  
Alan Williams           (finger alan at avocado.ucr.edu for pgp public key)
------------------------------------------------------------------------  
University of California, Riverside   "Where observation is concerned,
Dept. of Botany and Plant Sciences     chance favors the prepared mind."  
Alan at Avocado.UCR.edu                               -- Louis Pasteur
************************************************************************




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