sequence analysis software

Francis Ouellette francis at monod.biol.mcgill.ca
Tue Jun 16 17:38:23 EST 1992

Jan Kwiatowski (kwiatows at orion.oac.uci.edu) writes a loaded question :-)

>I would greatly appreciate hearing your opinion on commercially
>available sequence analysis software for IBM compatibles.
>What is the best?

here at "YEAST Chromosome I central" when we use a PC, we use PC/Gene.  
It is from  Intelligenetics (IG).  Their tech support email address is  ig-consult at presto.ig.com, and they would probably direct you to 
a sales person should you wish that.

Like many of the packages that are availlable it does it all (:^) ...
adequately.  A major reason why I like it, is because I know it (and 
I think you will get a lot of replies like that).  It has a vast array 
of DNA, RNA and protein sequence analysis you would expect from any 
commercial packages.   This is a straight DOS program (no windows here!) 
which we use on 386's and 486's.  It comes (should you whish) with a 
database which is not updated that frequently (2 times a year if I 
remember correctly).  It is able to import sequence from the standard forms. 

It is _very_ user friendly, with a very extensive menu system (uses the
mouse too), and  it is quite powerfull.  You will be able to input 
nucleic acids sequence in a variety of ways, and manipulate it or 
its translation products in ways that will make your head spin. 
(restriction maps, prosite analysis, CLUSTALL's alignment program, 
ASSEMGEL; the sequencing project gel merger just to name a few).

There are drawbacks  ...

Searches on the hardisk (should you have the space) or on the CD 
are both very slloooowww (even on our 33 MHtz 486), and I recommend 
your favorite fasta/blast mail server for that.  There are also lots 
of PD tools available for the PC which we still use routinely, like 
Eric Cabot's Eyeball SEquence Editor (ESEE, available at your 
favorite FTP site), and many many more ...

I understand that using a commercial package is done to avoid 
having to go from one package to the next, and one format to 
the next, but that would be"le meilleur des mondes possible" 
which we don't have yet, because we don`t all have unix boxes 
on our desks :)

All in all, I strongly recommend PC/Gene for the PC user, it has 
helped us in a lot of our analyses.  I have used the old IBI package 
many years ago, it did not compare.  I have used DNA* (star) and I 
did not like it as much.  UI have also used Beckman's package (now 
defunct I understand), I also did not like it as much.

A final word, about cost (although I am sure you would get a more 
accurate number from IG).  The package is about $3000, and if you 
want the service contract (software upgrades, database upgrades 
and _very good_ technical support), that will put you back another 
$900 or so per year.  I would not mind if that was a bit lower, and they 
give very poor deals on multiple purchases of the package, and 
it is not copy protected, but has the usual strict copyright 
message that comes with it...  (all these $ are CAN$$$).
Many programs are available on the net, and you can save a lot 
of money there, but you do not have the uniform "environment" 
and you have to reformat sequences in a different way for each 
package, and you would miss out on the tech support too.  
The PC/Gene manual is quite good too, and extensive.  
These are serious people, and they put out a good product.

As a caveat to all this, let me say that we have probably purchased 
every piece of software IG makes (pc/mac/Sun) and some of them in 
more than one copy (pc).  I, or anybody from my family, do not work 
for IG but I sometimes make recommendations to them about their software, 
which they always welcome.

well that was my can$0.02

best of luck,


| B.F. Francis Ouellette  
| manager, yeast chromosome I project
| dept of biology, McGill university, Montreal, Qc, Canada
| francis at monod.biol.mcgill.ca

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