sequence analysis software

Thomas L Sims tsims at magnus.acs.ohio-state.edu
Tue Jun 16 21:51:56 EST 1992

(and Francis Ouellette replies:)

>here at "YEAST Chromosome I central" when we use a PC, we use PC/Gene.

(lots of laudatory comments deleted)

>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 :)

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?

2. How do the stand-alone programs compare in terms of difficult computational
requirements to the on-line programs? For example--doing a combination of
pairwise and multiple sequence comparisons to find conserved/variable domains.
(I've done a series of multiple sequence alignments using UWGCG on our local
VAX lately for review articles I've been writing. The latest was a 24-gene
{amino acids} comparison of S-related RNases {about 200 aa} using PILEUP and
PLOTSIMILARITY programs from UWGCG. I'm now trying to do some 5' end dot-matrix
searches for potential regulatory sites (given that those searches are bogus
anyway). Can the PC-based programs handle these?

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?

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?

5. OK, one more. 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'm not talking about "squiggly plot" graphs like the 
UWGCG programs give, but something that actually lets you "see" the helix. I've
seen/used the output from Tony Croft's SEQANAL program (which is good!) that
lets you look at various aspects of protein structure comparison. I know that 
all of these programs are (basically?) guesses given the difficulty in going 
from 1-D chemical properties to a 3-D structure, so I'm not expecting the kind 
of data that you could get from X-ray crystallography.


Je veux le meilleur des mondes, s'il te possible. (Please correct my grammar!)

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

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