Best software package for various DNA analyses?
doelz at comp.bioz.unibas.ch
Mon May 22 02:52:21 EST 1995
SamiPekka Heikkinen (spheikki at messi.uku.fi) wrote:
: We are interested in purchasing a software package to do various analyses on
: DNA ie. restriction site searches, primer and probe design, sequence analyses
: etc. We are using PC's. What are my choises and which is the best to your
1. You may ask the Finnish EMBnet node at CSC (Heikki.Lehvaslaiho at csc.fi)
Centre for Scientific Computing, Espoo, Finland
2. Find out what your demands and resources really are.
o Mainframe: Look at GCG (Genetics Computer Group) and Intelligenetics.
Don't take 'mainframe' seriously, a moderate workstation on the desk
will do. Both packages are commercial and database updates are available
from the vendors or you may do it yourself with GCG. Neither of the
two will do Genome work in mapping and contig localization, you will
need separate software for that (acedb or a derivative thereof).
o PC/Mac: Be aware that professional packages from the vendors require
licenses if purchased commercially, and, even network licenses, become
possibly more expensive than the 'mainframe' solutions above. For the
server to run the package a very high-end PC/Mac is urgently recommended,
i.e. you should go with a system in the workstation range rather the
off-the-ramp entry model.
o Public Domain/'freely' accessible software: Many programs can be accessed
from the internet as 'search servers' or can be downloaded 'free'. Make
sure that you know what you're facing, though, as no interoperability
guide with maintenance will make things easy. It is a cheap but very
rough road you are going, then.
3. We use the GCG package for years now, and our 300 researchers are pleased
with that, installed on UNIX or VMS systems. Actually, we started the UNIX
version on a moderately small machine (3 GB disk, CD-ROM, 48MB memory) some
years ago but prices have come down and systems are more powerful today.
The real cost-raising factor is human support, and, depending on the
choice in (2) might be considerable. This is (a) for database updating
and program maintenance, and (b) for _user_ support and teaching.
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