sequence analysis software

Francis Ouellette francis at monod.biol.mcgill.ca
Wed Jun 17 13:22:21 EST 1992

Thomas L Sims (tsims at magnus.acs.ohio-state.edu) writes:

>I've got a few follow-up questions (I'm in the market too).
>1. How do the stand-alone programs compare price-wise to the on-line programs
>(i.e. UWGCG or Intelligenetics IG-Suite)? I'm _not_ talking about having a site
>license on your local VAX or Unix machine, with a system manager etc., but in
>terms of (poorer) sites where one would have to telnet to a remote site for the
>service. Does the cost for cpu minutes for searches/sequence comparisons
>eventually equal/surpass the stand-alone price over the course of 3-5 years?

Well I am sure this will vary from site to site.  I know that a lot 
of institutions (this one among them) will provide "free" Internet 
access to its reserchers, so I guess it would take a few years to 
catch up to the price of a PC!  But let me rapidly add (so to avoid 
missunderstandings) Internet is not free, it cost, but some school 
pay up and do not transfer the cost to its users.  This may not 
last forever.

>2. How do the stand-alone programs compare in terms of difficult computational
>requirements to the on-line programs?

I am not sure about the limit of CLUSTALL (in PC/Gene or the PD 
version) is, but I am sure it is beyond 24.  I am sure somebody 
will correct me if I am wrong :-)

>3. Do 386/486 machines give you a substantial speed increase using the
>stand-alone programs versus slower machines? I've always had the impression
>that the PC-programs were written for AT machines (based on economic realities)
>and couldn't really take advantage of the greater processing speed/memory
>available in newer machines?

It is very true that very few packages take advantage of the multi-
processing capacity of the 386 and 486, but with these higher-end 
models you also get "faster" (the MHtz number) performance with 
"cheap" 50 MHtz/486  on the market ...  I assure you, you will 
see a difference.  

(action of opening a can of worms ...)

But without wanting to get into the ball going on this subject 
(again!) maybe a low end workstation is an alternative to a PC 
buyer.  There is a lot of "front ends" for public domain (PD) 
software out there, GDE for example.  A wonderfull piece of 
work which lets you use all sorts of PD software.

>4. Last, does anyone know if there are any programs (being) written to take
>advantage of OS/2 2.0 or Windows 3.1 environments?

I don't know of any for OS/2, but maybe you could ask your Pharmacia sales rep about this one, as their ALF sequencer works under OS/2 ... they may know ... My Pharmacia Sales rep did not know of anything 6 months ago.  They actually included (back then) the DOS DNA* with their package ...

As far as window 3.*  there is the NCBI "entrez" and "Macaw" available from  ncbi.nlm.nih.gov.  Very nice packages.

>5. OK, one more. 

OK, some of us do have to get back to work ...  ;-)

>Does anyone know about (stand-alone or otherwise) programs 
>that can give you a graphical display of predicted protein structure from amino
>acid sequence data? 

I don't know of any for the PC, but would like to look at any you may find ...

>Tom Sims
>tsims at magnus.acs.ohio-state.edu

you are welcome,

>Je veux le meilleur des mondes, si il est possible? 



| 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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