Which sequence analysis package?

unknown at dl.ac.uk unknown at dl.ac.uk
Fri Jan 7 12:55:45 EST 1994


I recently evaluated several of these packages and had similar
impressions.  Among all the packages(PC pakages), I found that DNASTAR
was the best in terms of having robust algorithms and a reasonably easy
interface.  However, as of 1993, use of the program required a keydisk
and the licensing provisions stated that the package could be used on
one, and only one computer.  We do not buy packages that have copy
protection (especially dongles!) because they almost always cause
problems, and having to physically move files every time we wanted to
analyze them is annoying.  The hitachi package had the best interface,
but was weaker in terms of the algorithms used for sequence analysis. 
The licensing provisions for this package were extremely reasonable in
that they allowed one to use the package on more than one computer
*providing* that these machines were in the same laboratory.  This type
of stipulation is most reasonable for the academic lab.

In the end, I decided to buy none of the packages because the cost was
relatively high, and the interfaces for the PC versions were not good
enough.  It's just as easy to telnet to our Vax that is running GCG.

If you are set on buying one of these programs, and don't mind copy
protection etc., I would recommend the DNAstar package.  I used it when
I was a postdoc, and found that it worked quite well.

> In article <59045 at sdcc12.ucsd.edu>, me28tl at sdcc12.ucsd.edu (tzu-ping lin) 
> writes:
>  
> > Hi, everyone.  We are currently using PCGene from IntelliGenetics 
> > and Beckman Gelmate to digitize sequencing gels and do sequence 
> > analysis.  The digitizer is old and not working well and the 
> > program is very difficult to use.  We are considering purchasing 
> > a new package.  We are considering MacDNAsis from Hitachi and 
> > GeneWorks (or new PC Gene) from Intelligenetics.  Does anyone 
> > have any experience with either of these systems?  We need a 
> > system that's easy to enter sequence from gels and easy to use. 
> > 
> > Any suggestions welcome.  Also, we have both Mac (LC III) and PCs 
> > (386 and 486 varieties) in the lab.  Which one do you think is 
> > a better machine for sequence analysis in terms of hours power, 
> > ease of use, etc.  Thanks. 
> 
> Currently, there is a better choice of these programs for Macintosh than for 
> PCs.  Examples of Mac programs include GeneWorks 2.2.1 from Intelligenetics 
> (fax 415-962-7302); MacDNASIS 3.0 from Hitachi (fax 415-615-7699); MacVector 
> from IBI/Kodak and DNAStar (don't have their numbers).  I think that the 
> situation may change soon as most of these companies are working on Windows 
> versions.  However, these versions are likely to be very simlar to the Mac 
> versions.  This is a very competitive market.  In truth, it can't really 
> sustain four major commercial products especially when you consider the price 
> (around 3,000 bucks for each program), the fact that most people have access 
> to GCG on a Vax or Unix network and the existence of some very good 
> shareware/freeware programs.  Examples of the latter for the Mac are SeqEd 
> and (my favorite) DNA Strider 1.2.  The nice thing about the commercial progs 
> is that they "do it all" and are stand alone.  The not-so-nice-things are 
> their dependence on CDROM for database searches (and you have to subscribe to 
> program-specific updates at relatively high cost) and their understandable 
> copy protection schemes.  Several use "dongles" which plug into the ADB port 
> of the Mac.  In our group, each member uses different Macs so it would be too 
> inconvenient to shift the thing around yet the program would probably not 
> need to be used concurrently so the expense on buying an extra dongle is 
> difficult to justify.
> 
> If you really need a standalone package then try them out first.  I think all 
> of the companies have time-limited or feature-limited (i.e. can't save or 
> print) demos.  I've tested GeneWorks and DNAStar and played with MacVector.  
> All are relatively easy to use on the Mac (much more intuitive than GCG) but 
> each has advantages and disadvantages and uses slightly different metaphors.
> There is also a small "magazine" called Biotechnology Software which tends to 
> review the packages every so often (I don't know the source).
> 
> I decided to hold off buying for these reasons.
> 
> DNA Strider (by Christian Marck, 200 bucks to register) lets us do 
> restriction digests, reading frame searches, protein prediction, etc.  SeqEd 
> has a contig alignment algorithm and can do Clustal matches (it is likely 
> that most of the commercial packages use similar core algorithms). NCBI has a 
> blast server (there is a neat little Hypercard front end that automates 
> searches and retievals) which is updated nighly rather than every 3 months 
> for the CDROMS.  You can also subscribe to Entrez via the NCBI (about 80 
> bucks for 2X6 CDs a year).  This allows for reference and sequence searching 
> (but is only a selection of the databases as far as I can tell).
> 
> So we can do most stuff from each of the Macs (and have access to GCG if need 
> be). If the copy protection was different (say network sensitive) and you 
> could search any CD, I would reconsider.
> 
> Anyway, although biased by use, I'd say the Mac packages are the best bet for 
> now.  In 6 months it may be very different.
> 
> Jim
> 
> (who obviously has no connections with any of the companies mentioned)
> 
> 
> 
> 
> 
> 

==============================================================================
James F. George, Ph.D.              "Back off man, I'm a scientist"
Department of Surgery                --Bill Murray
University of Alabama at Birmingham
205-934-4261 voice
txpljfg at uabcvsr.cvsr.uab.edu
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