Cloning Software

Geronimo user at server.com
Mon Jun 2 03:59:07 EST 2003


Sum, ergo cogito: along the line of reasoning that you propose one would
choose the automobile to travel to the Moon simply because most people
travel by car.

Five years ago I tried to develop algorithms for cloning on Unix. It turned
out a thorough cloning analysis requires a lot of CPU power... and memory.
The Vector NTI Suite is a joke cloning-analysis-wise, like it is for
choosing primers. In proof of the latter try concatenanting the sequences of
the known mouse actin cDNAs and then choose primers to amplify within the
beta-actin messenger; Vector NTI will never give you primers that work (did
that first, wasted a lot of PCR cycles, Taq pol, etc.) but GCG will and your
*will* get a product of the right size in your PCR using GCG. But it's so
much simpler using a desktop solution such as Vector NTI, isn't it? Except
it doesn't work.

Now, back to Perl. I use Perl 95% of the time I do programming. And I do
that a lot. And I seriously doubt it's the right tool for cloning software.

Pax vobiscum... Hic! In vino veritas! ;)


"Ergo Sum" <google at home.com> wrote in message
news:qY8za.130068$nA6.1444642 at charlie.risq.qc.ca...
> Geronimo wrote:
>
> > You may wish to try this first:
> >
> >   http://topaze.jouy.inra.fr/cgi-bin/CloneIt/CloneIt
> >
> > I like your idea. The cloning algorithm is likely CPU-intensive, Perl
may
> > or may not be up to the job. :)
> >
>
> PERL might not be the best choice, except that its the most used one in
> biology and bioinformatics. Check the Bioperl site:
>
> http://bioperl.org/
>
> I would hate an early schism on this project, since I deem it is long
> overdue to the biologist community an open source program for cloning.
>
> IMHO PERL might not be the most performant choice, but might turn out to
be
> the most accessible and the easiest path.
>
>
> -- 
> Aquila delenda est





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