The oligos designed can be BLAST searched, to verify their specificity. Specific oligos are designed by avoiding regions of significant homology found by automatically interpreting BLAST search results. "Minimal Set", one of the features in AlleleID, helps design the fewest number of primers and probes that identify each of the desired species/strain/taxa from the mix.įor taxa or cross species assays, this feature is useful when the group or taxa is highly dissimilar.įor a partial set of pre-designed or published set of primers, AlleleID can design compatible primers and probes for the rest of sequences for species or taxa specific assays.ĪlleleID employs a sophisticated algorithm to assure assay success. This functionality can also be used for detection, identification, quantification of contaminants. For cross species assays, AlleleID identifies conserved regions of related organisms that can be used with samples from any of the organisms. The assays are designed to detect only the strain or species of interest from the mix. To design species identification assays, AlleleID aligns sequences using ClustalW and analyzes conserved and species specific regions to design molecular probes for microarrays and TaqMan ®/molecular beacon real time PCR assays. We are proud to have organizations such as FDA, CDC, and USDA as our customers." "We are pleased with how well AlleleID has been received by researcher all over the world. "AlleleID can be effectively used in developing assays for biodefense, environmental monitoring, prevention/control of infectious diseases, development of surveillance tests and biodiversity studies," says Kay Brown, V.P. In addition to designing single template and multiplex experiments version 4 includes support for designing species identification and taxa discrimination assays for real time PCR chemistries such as SYBR ® Green, TaqMan ® and TaqMan ® MGB (Minor Groove Binding). Junction probes span exon-exon boundaries while intra-exon probes lie entirely within a single exon, making AlleleID an effective tool in designing experiments to test splice forms. To detect the alternative splicing events, AlleleID designs two types of probes called junction probes and intra-exon probes. Premier Biosoft International has announced the world wide release of version 4 of AlleleID, tool designed for designing diagnostic assays for both real time PCR and microarrays.ĪlleleID now includes support for designing probes for splice variant arrays.
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