Primer design

Tom Anderson univ0938 at herald.ox.ac.uk
Wed Nov 27 19:04:40 EST 2002


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. .,




More information about the Methods mailing list