MacVector vs DNASIS vs ?

Reinhard Doelz doelz at comp.bioz.unibas.ch
Tue Jan 24 00:52:01 EST 1995


Carl Lawyer (clawyer at SIUMED.EDU) wrote:
: Overall, none of the available sequence analysis programs is perfect and
: what is needed is big dollar investment for evolution of truly good
: computer tools. The sequence information being generated by the genome
: project cannot be fully utilized for improving human health unless much
: better user friendly and readily accessible (non-VAX requiring) programs
: are developed.

Just to mention that there are these packages, including the Genetics 
Computer Group Package, and the Intelligenetics Suite. Both are known to 
run on workstations which became pretty affordable these days. The term 
'VAX requiring' might be misleading. The GCG programs, for example, feature 
a X-based user interface and run on far more than the VAX operating system -
not to mention that Digital's new hardware is called 'AXP' and runs VMS as 
well. At least in the US, you will get a reasonable low-end workstation 
for your personal use at prices which are similar to the top line of the 
PC business. Just don't buy a lab computer with speakers and multimedia 
systems but change to a workstation if you don't have a reasonable site 
close to you where you can work. Europeans might benefit here as we have 
the EMBnet national nodes offering access to these packages at remote 
login to their national users. The list of EMBnet nodes is available 
on WWW, as part of the embnet.news newsletter. Check out the electronic
version at http://www.ch.embnet.org/embnet.news/info.html or ftp your post-
script copy from ftp://ftp.no.embnet.org/pub/embnet.news/embnews2.ps 

Another issue coming up is that sequence databases are truely nice but much
information evolving from the increased sequence data is stored in 
'auxiliary' databases. The software packages mentioned do not cover 'all' 
databases sufficiently well. The SRS package (a call for votes is currently
open) is capable of integrating these databases into a unique cluster pool
of information. Those of you who haven't used or heard from it, check out 
the network servers. Last I counted 11 sites and 57 databases were available.
(URL: http://www.embl-heidelberg.de/srs/status.html). SRS runs locally as 
well, on many sites in Europe and a few in the US. It is available via
anonymous ftp from the author (Thure Etzold , EMBL Heidelberg). 

Something which is important to be pointed out in this context is the use 
and access of the data. It has been mentioned that Entrez and Blast are 
'cheap'. Both may be run locally on local resources and might require a
substantial investment if data and software are to be maintained locally. 
The end user will require at least three CD-ROM drives attached to the local
PC or mac if he/she wants to work with data efficiently. Neither Entrez nor
some of the other packages are designed for the 'all and everything' and the 
user will require to use the network. Europe, in particular, suffers from 
extremely high telecommunication costs which are not currently paid by the 
biological community. Keep this in mind if discussion software and data 
access without even mentioning that there is some hidden cost involved. 
I don't want to tap you but keep in mind that 'cheap' nets are payed for 
elsewhere. 


Regards
Reinhard Doelz

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