Useful bookmarks
for probe and primer design:
http://www.operon.com/oligos/toolkit.php
Use free
online Tm calculators to see what the Tm for primer and probe sequences are.
We use the Operon calculator, as it also has a good tool to check possible
primer-dimerization sequences. Reach it from www.operon.com then
select DNA Synthesis, then select Oligo Toolkit.
http://www-genome.wi.mit.edu/cgi-bin/primer/primer3_www.cgi
This is a
link to Primer3 software. It is software that allows for primer design and
also helps picking an internal oligo sequence to these primers (a probe sequence).
Like most primer design algorithms, it has the disadvantage of not
taking into account secondary structure issues that are paramount in
primer/probe design for real-time PCR. With that caveat in mind, it is a good place
to start the design process, if you are not inclined to do it by eye (i.e. scanning the
sequence yourself). Then you can check your sequences at the folding site (described
below).
http://www.ncbi.nlm.nih.gov/BLAST/
This is the site
for the Basic Local Alignment Search Tool from the National Center for Biotechnology
Information. Use this site for checking specificity of probe and primer sequences.