AlleleID 1.01

AlleleID 1.01
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AlleleID aligns sequences to locate differences in DNA and to find
conserved regions, to design qPCR assays for taxa discrimination
and species identification.

Feature Summary:

Related Gene Assays: Designs species specific, taxa
discrimination, cross species TaqMan probes and molecular beacon
for pathogen identification, strain discrimination, genotyping
and biodiversity studies using qPCR.

Species Specific Assay Design: Designs primers and probes for
species identification aligning sequences using ClustalW. It
then analyzes conserved and species specific regions to design
primers and probes to amplify only the species of interest.

Taxa Discrimination/Cross Species Assay Design: Designs a
single (common) probe and primer pair to identify a taxa or a
group of organisms from the mix. The program limits the search
to conserved regions. When such designs are not feasible, the
program attempts the design by minimizing mismatches.

Selective cDNA amplification: Avoids gDNA by designing primers
across exon junctions. The exons are identified by interpreting
GenBank header annotations or by specifying them manually.

qPCR Assays: Designs optimal SYBR Green primers, TaqMan
probes, FRET probes or molecular beacons for real time qPCR
assays. Designs single or multiplex TaqMan and beacon assays
for allele discrimination or gene expression studies. Allele
discrimination SYBR Green and FRET assays can be designed as
well.

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