I am doing a lot of real time PCR these days. (TaqMan based) but this is a relatively new field for me. I am trying to PCR amplify a gene from plasmodium which I think is involved in host gene silencing. Can anyone guide me to a design tool? RTPrimerDB does not have what I require...
Any help would be appreciated.

Hi there,

I haven't had to design primers myself for quite a while, but since the last time a lot of tools have appeared. Just doing some quick looking around turned up this very useful web page on the topic
http://molbiol-tools.ca/PCR.htm
which provided the following links to free design software:

free
Primer3 at these two sites
http://frodo.wi.mit.edu/cgi-bin/primer3/primer3_www.cgi
http://biotools.umassmed.edu/bioapps/primer3_www.cgi

GeneFisher
http://bibiserv.techfak.uni-bielefeld.de/genefisher/

PCR Now
http://pathogene.swmed.edu/rt_primer/

I'd be curious to hear if any of these tools help, please let me know.
-Ben

Hi Froglet,

Thank you for the wonderful Southwestern Medical Center site. I got two very promising primer sets for my sequences. In addition my PI (Dr. Herbert Fischer) decided to purchase AlleleID from Premier Biosoft. Though I haven't as yet tried this out as yet, but seems promising with primer and taqman design on aligned sequences and the alignment tool is built-in. what more, it supports microaary design as well and Blast.

The price though (3885 US dollars) is on a higher side. I'll test the primers post Christmas and will write about it here.

Hi RealTime PCR,

I was in a similar dilemma when I was looking forward to evaluating some tools for designing molecular beacons for SNP genotyping. The sequences were quite bulky and one of my lab mates wished to do a multiplex of 4 genes. Now I had no options for beacons as no free tools do an accurate beacon design. But when I went to the Biosoft site, I found Beacon Designer( and AlleleID of course). Both of them have Beacon design option and Beacon Designer also supports NASBA for mol beacons. Now this tools is, let me tell u, a real time saver. I got in touch with the company and tried the tool for a week. The beacons are yet to be lab tested but appear nice with no dimers/runs and acceptable G/C ratio.

This tool is comparatively lesser priced at 1885 and an year of maintenance free! I'll purchase it. Do share your AlleleID experience with me.

AlleleID turns out to be my tool of choice for TaqMan Design and design of real time pcr primers for Bacterial Identification. Also try out the BD free Edition