msatcommander versus invitrogen's website

[brant]

Hi,

glad you were able to get everything setup and running.

1.) the tagging option is used for a relatively cheap method of
polymorphism testing. See Glenn and Schable 2005 (Methods in
Enzymology) for a summary or Boutin-Ganache et al. 2001 for the
original method. Glenn and Schable modify Boutin-Ganache's M13 for an
M13R and add the CAG tag.

2.) the modification of distance to 20 from 50 will only change the
distance between msat repeats that are combined (to form compound
repeat(s)). This does not change the distance with which the repeat
is buffered during primer design (this is set by default within the
code). Primers are then chosen to fall within certain size classes
(150-250, 100-300, 301-400, 401-500), in that order.

3.) you may, indeed find primers that invitrogen's site cannot.
Their primer design code is proprietary, and I cannot tell you how it
works (for this reason). The primer design code that runs within
msatcommander is primer3 (http://primer3.sourceforge.net/) which has
been tested and used on a number of projects (search for primer3 on
google scholar: http://tinyurl.com/ynubwc). I also work with this
project on the maintenance and upkeep of primer3, and am pretty
familiar with its features/limitations.

You may be seeing more primers from msatcommander that you do not get
from invitrogen due to invitrogen's primer picking parameters which
are probably strict (again, no idea on their defaults).

Those for msatcommander are also relatively strict and can be seen
here:

http://code.google.com/p/msatcommander/wiki/PrimerDefaults

As for the number of primers returned and profit maximization for
Invitrogen, I can't really say. I do agree that it would behoove them
to return more primer pairs. That being said, as a company providing
a service, they are responsible for the output that is returned (and
losses that may/may not be incurred). So, it pays for them to be very
conservative.

As with everything else, there is a tradeoff here. I have chosen to
return more primer-pairs, some of which may not work (as the number of
pairs designed increases, you will see a few failures). That being
said, we have seen roughly 85% amplification success, which is good-
excellent.

If you combine this with the automated nature of the program, tagging
of primers for testing (versus directly labeling), and the time (cost)
associated with slower methods of primer design (single primer via
Invitrogen/IDTDNA/Oligo), everything comes out pretty equally.

If you only have a few sets to design and a small amount of data *and*
you _must_ maximize success, perhaps a tool such as that provided by
Invitrogen (or an even better tool like Oligo 6.0) may be the ticket.

hope that helps,
b


On Tue, Dec 11, 2007 at 08:22:05AM -0500, __ wrote:
> Brant
>
> Just had my first opportunity to really use msatcommander last night. Had
> issues getting everything to run (user error, not programming) and then when
> I got the output, I wasn't certain that my initial setup was correct. I had
> it search for everything except the monomeric repeats, but turned off the
> tagging functions (because I couldn't remember what, specifically, that was
> all about) and I believe I modified the default of 50 to 20 (in primer
> design, distance) but again, I don't remember what this function
> specifically relates to.
>
> It seems to find primers that specific sites like Invitrogen can't. I
> assume that the program is designed to do this, but it seems strange to me
> that a site that is built on sales can't maximize their profits, if you know
> what I mean! ;-)
>
> If you have just a moment, could you clarify for me?
>