AlleleID.
It is designed to address the challenge of pathogen detection, species identification and taxa discrimination using TaqMan and molecular beacon assays. With ClustalW multiple sequence alignment at its core, AlleleID can help design universal or taxa/species specific primers and probes. All major qPCR assays including molecular beacons, TaqMan, FRET or SYBR Green are supported. It uses BLAST search to assure specificity. To assure assay success, AlleleID uses template folding to avoid locating primers in the secondary structures of the template.
With AlleleID, you can avoid gDNA by designing primers/probes across exon/exon boundaries. The intron exon regions are identified by interpreting GenBank annotations or by specifying them manually.
To get started quickly with AlleleID, please download and listen to the multi-media tutorial:
http://www.PremierBiosoft.com/DATAFILES/AL100Tour.exe.
Then please download the demo version of the program from:
http://www.premierbiosoft.com/DATAFILES/AlleleIDTour.exe
