Best software package for various DNA analyses?

Reinhard Doelz 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
: experience?

In brief; 

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. 

Reinhard Doelz
EMBnet Switzerland

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 Biocomputing        CH 4056 Basel| electronic Mail    doelz at ubaclu.unibas.ch|
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