DNA software HELP!!!

eric anderson e-anderson at ski.mskcc.org
Sun Jan 5 17:14:44 EST 1997

In article <5aokp7$mrg at news.xs4all.nl>, marker at xs4all.nl (Niels Groot) wrote:

> In article <5am677$jfb at eldborg.rhi.hi.is>, thorarb at rhi.hi.is says...
> >
> >Hi there.
> >
> >My lab is about to invest in DNA analysis software  for PC and we would like 
> to
> >see comments on the latest programms in that field. The programm must have
> >the general tools like multiple alignment, restriction mapping, translations 
> >etc, and be user friendly when working with files from the main
databanks, or 
> >when transfering them to other programms like Word.
> >We have heard that DNASIS 2,0 for Windows is good but we would like to have 
> >comments/critics on it and other programms, if you would be so kind, 
> >because we don't want to throw away $2500 for something we can't use.
> >Thanks in advance.
> >        Thorarinn Blondal
> >        Institute of Biology
> >        University of Iceland
> >        E-mail: thorarb at rhi.hi.is
> >
> >
> Take a look at SeqSearch v1.1. This package is not so sophisticated as DNAsis 
> but offers some features that other packages don't have besides the normal 
> routines as restriction analysis. Moreover, the price is less than 20%
of thae 
> price of DNAsis. Some features are:
> - Multi user/project storage
> -Sequence storage in multiple databases:   
> sequences/plasmids/constructs/oligo's and motifs
> - Restriction analysis with pre-defined and user-defined enzym sets
> - Mismatch primer design
> - Mutagenic primer design for codon substitution mutagenesis
> - Silent mutagenesis
> - Clone Bench for designing constructs
> - Fragment analysis with gel pattern simulation
> - Hydrophobic plot of proteins
> - Motif search on DNA sequences
> - Oligo Info
> - Reading frame analysis
> For more info and the latest release of SeqSearch v1.1 please check:
> http://www.xs4all.nl/~marker
> Niels Groot
> marker at xs4all.nl

it should also be pointed out that Niels Groot appears to have a vested
interest in your purchase of SeqSearch v1.1.  not that this nullifies the
validity of his claims, but he should have made such a disclaimer.  having
never tried the product, i can't say whether or not it's good, but at
least there's a demo version available on Niels Groot's website.

my reccomendations for sequence analysis programs are: 

GeneWorks/PCGene from Intelligenetics:  this is/was pretty crash prone on
68K Macs but i haven't every used it on a PPC or a Windows machine so i
can't vouch for it's stability on those platforms.  it is however pretty
powerful, doing everything that you say you want it to do and more.  in
fact, it may be too powerful for you.  but there is a demo version of it
at the indiana website so give it a shot.  it's also pretty expensive but
upgrades are cheap and frequent.

Sequencher vSomething.Something:  I have only tried demo versions of this
but i really liked it.  unfortunately both people that i have tried to
convince to buy it have their money tied up in a long term license with
the miserable MacVector program from IBI so i haven't had a chance to try
the full version.  it's very easy to use, very stable and pretty
inexpensive.  it doesn't do everything that DNAsis and GeneWorks/PCGene
do, but it does everything i've ever wanted it to do.  i also don't know
for sure if it's available for Windows.  but there is a demo version at
the indiana site (i think).

i have no connection with any of these companies as anything other than a
former user of their products.

good luck choosing a program.  


Eric C. Anderson
Memorial Sloan-Kettering Cancer Center
Sloan-Kettering Institute
1275 York Ave. Box 470
New York, NY  10028
(212) 639-2977
e-anderson at ski.mskcc.org

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