Primer design

EK khatipovNO-SPAM at NO-SPAMuchicago.edu
Thu Nov 28 18:05:20 EST 2002


18-25 bp in length with no more than a half of GC. That's the simplest rule
that I am sure worked for many. What is the source of your DNA?
Emir

"Phoenix" <ddboyboy at she.com> wrote in message
news:as5i6p$2gqq$1 at ijustice.itsc.cuhk.edu.hk...
> Thanks very much : )
> I'll try that software
>
> Another question want to ask
> I would like to know the succcessful rate of the primers designed by
primer
> 3 in PCR?
> Coz i usually fail in PCR if i decide primer by myself and need to order
> several pairs of primers : (
> so i wonder if there is any good software for primer design at the
beginning
>
>
>
> "Tom Anderson" <univ0938 at herald.ox.ac.uk> ?????
> news:Pine.OSF.4.44.0211272353430.9705-100000 at ermine.ox.ac.uk...
> > On Wed, 27 Nov 2002, Mark Silby wrote:
> >
> > > Hi, you could try "Primer 3"
> > >
> > > http://www-genome.wi.mit.edu/cgi-bin/primer/primer3_www.cgi
> >
> > primer3 is really intended for designing pairs of primers which amplify
> > ~200 bp amplicons within a region of interest - the sort of thing you'd
> > use for diagnosis, or characterising clones or something, rather than
> > primers you'd use to amplify the region itself. you can persuade it do
do
> > that, by giving it the right parameters, but it tends to take rather a
> > long time - i was interested in an amplicon of ~20 kb, and i ended up
> > leaving it overnight!
> >
> > > Or look at the following for more mol biol tools.
> > >
> > > http://www.r9corporation.fsnet.co.uk/
> >
> > excellent links!
> >
> > i quite like WebPrimer:
> >
> > http://genome-www2.stanford.edu/cgi-bin/SGD/web-primer
> >
> > although i can't say how it compares to the other tools, most of which i
> > haven't used.
> >
> > has anyone used prima from the emboss package?
> >
> > tom
> >
> > --
> > an optical recording release. copyright digitally mastered. .,
> >
>
>





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