Cloning Software

Ergo Sum google at home.com
Mon Jun 2 03:59:44 EST 2003

Geronimo wrote:

> 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! ;)

I humbly accept the corregitur. Give headway to experience.

I'm quite curious to see what Pierre Lindenbaum has in for us before looking
more in the details.

By the way, I was not proposing an automobile for going to the moon, but
something more like a network of Linux based 486s to subsitute Mission
Control in Houston ;)

As for the GCG solution, my problem is the same that for Vector NTI. It's
not the desktop solution that helps, its the open source. I work on a Linux
based system, and use EMBOSS and STADEN for most of my BioMol planning. Out
of luck, the cloning applications are lacking.

If one would make a ladder using all the material used for cars, we might
just build an elevator instead of a ladder to the moon. ;)

Quo usque morituri te salutam.

Aquila delenda est

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