OLIGO Software Package for PCR Primer Selection
Kevin G. Korth
selection and one package that we are leaning toward is OLIGO (National
Biosciences) [advertised heavily in Bio/techniques]. However, I have
heard some negative feedback on how well the primers work that are chosen
versus ones that are chosen manually. I don't know whether to believe it
or not.
Has anyone out there in cyberspace used OLIGO (or a better package)
and would be willing to send me some input before I fork out the $1.2
grand to purchase the package??
You can E-mail me directly at kko...@kcc.com or post. THANKS!
Kevin Korth
Molecular Biology Division
Corporate Microbiology Group
Kimberly-Clark Corporation
Susan Mango
We've been using "primers". for one thing, it's free. for another, all
the primers I've made so far have worked-- a grand total of 8 or so.
you can get it from the IU biological archives. good luck, susan
University of Wisconsin - Madison
sma...@macc.wisc.edu
Chihiro Yamada
<kko...@kcc.com> wrote:
> We have been evaluating software packages to assist in PCR primer
> selection and one package that we are leaning toward is OLIGO (National
> Biosciences) [advertised heavily in Bio/techniques]. However, I have
> heard some negative feedback on how well the primers work that are chosen
> versus ones that are chosen manually. I don't know whether to believe it
> or not.
>
> Has anyone out there in cyberspace used OLIGO (or a better package)
> and would be willing to send me some input before I fork out the $1.2
> grand to purchase the package??
A colleague of mine (David Micklem) designed some degenerate primers and
screened them by eye. Most of them didn't work. So I then designed some
more, this time using OLIGO to help, it didn't seem to increase the
proportion of primers that worked. When I went back and check mine and
Davids primers on OLIGO to see if the ones that had worked had anything in
common, there seemed to be no relation between OLIGOs various different
methods of measuring quality, and the primers that worked. i.e. some of
the primers that didn't work looked better when examined by OLIGO than
ones that did work et vice versa.
It didn't fill me with much faith in OLIGOs ability to choose good primers....
ho hum.
Chihiro
_/ _/_/_/_/_/ / Chihiro Yamada.
_/ _/ _/ _/ / c...@mole.bio.cam.ac.uk
_/ _/_/_/_/_/ / Cambridge, United Kingdom
_/ _/ _/ _/ _/ _/ / "Do Earwigs make Chutney? .....
_/_/_/_/_/ _/_/_/_/_/ / ...NO!!" Eddie Izzard
GS d--- H s-:- g+>- p? !au a23 w+ v+?*@ c++ U P? !L !3 E? N+(++) K !W-- M+
!V po(-) Y t+ !5>+ !J R+ G++@ tv@ b++@ !D B? e+++ u-*@ h*-- f+ r n+(----) y+
Dr. Massimo Romani
included in the GeneWorks package sold by Intelligenetics, running on
Macintosh (unfortunately it is quite expensive, at least in Italy). We
have conducted parallel runs with PRIMER 0.5, which runs on Unix
machines, with absolutely identical results (except speed but if you are
scanning a sequence shorter than 10 kb this is not a big problem).
Best regards
Massimo Romani
Istituto Naz. Ricerca sul Cancro
IST-Genova
Dr. Massimo Romani
AShaw5
am very unhappy that I bound them. They are not very intuitive to use and
for what I want (to make mutagenic oligos) they are a pain. I think that
we still make most of our oligos by eye. It works just as well or better.
Andrey Shaw