DNA software for Linux

Keith James k.james at bangor.ac.uk
Fri Jan 9 07:19:13 EST 1998


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>>>>> "January" == January Weiner <jweiner1 at ix.urz.uni-heidelberg.de> writes:

    January> Hello, we are currently using Mac DNA Star enviroment in
    January> our work. I wondered if there are any such programs for
    January> Linux - i.e. sequence editing, finding restriction sites,
    January> oligonucleotides for sequencing, sequencing project
    January> management and such.  Thank you in advance!  January
    January> Weiner 3

There are quite a number of programs: GDE (editing, customisable interface
for other progs), FSAP and tacg (restriction and seq analysis), Primer3 
(PCR) primer design, CAP (contig assembly), xbbtools (GUI environment),
SeaView/PhyloWin (phylogenetic anaysis), ClustalW & X (multiple alignment).

Good places to look:

Molecular Linux page at http://evolution.bmc.uu.se/~thomas/mol_linux/
EBI catalogue at http://www.ebi.ac.uk/biocat/biocat.html

tacg2 is great and is at:
http://hornet.bio.uci.edu/~hjm/projects/tacg/tacg2.main.html

Much of the software at EBI is available as C source which will compile
with gcc if there are no pre-made binaries. GDE is nice because you can
customise the menus to give direct access to command line progs which
will then return their output to the GUI. I've found that a well-configured
GDE wipes the floor with our Windows DNAStar.

My homepage has a shell script for converting DNAStar files to Fasta format
which you may find useful if Mac DNAStar files are the same format as the
PC DNAStar ones. Hope this helps.

- -- 
Keith James Ph.D. - k.james at bangor.ac.uk - http://www.bangor.ac.uk/~bss194 
Biodegradation Group - School of Biological Sciences - University of Wales
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