Premier Biosoft International has released version 4 of AlleleID, the only tool that helps design microarrays and real time PCR diagnostic assays for pathogen detection or bacterial identification
The new version includes support for designing splice variant microarrays to detect gene splicing and alternative splicing events.
Premier Biosoft International has announced the worldwide release of version 4 of AlleleID, the only tool available for designing diagnostic assays for both real time PCR and microarrays.
AlleleID now includes support for designing probes for splice variant arrays.
To detect the alternative splicing events, AlleleID designs two types of probes called junction probes and intra-exon probes.
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 novel splice forms.
In addition to designing single template and multiplex experiments version 4 includes support for designing species identification and taxa discrimination assays for popular real time PCR chemistries such as SYBR Green, TaqMan and TaqMan MGB (minor groove binding).
"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, VP business development and marketing.
"We are pleased with how well AlleleID has been received by researcher all over the world.
"We are proud to have organisations such as FDA, CDC, and USDA as our customers".
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.
The assays are designed to detect only the strain or species of interest from the mix.
For cross species assays, AlleleID identifies conserved regions of related organisms that can be used with samples from any of the organisms.
This powerful functionality can also be used for detection, identification, quantification of contaminants.
Minimal Set, one of the most innovative features in AlleleID, helps design the fewest number of primers and probes that uniquely identify each of the desired species/strain/taxa from the mix, lowering assay costs.
For taxa or cross species assays, this feature is especially useful when the group or taxa is highly dissimilar.
For 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.
AlleleID employs a sophisticated algorithm to assure assay success.
Highly specific oligos are designed by avoiding regions of significant homology found by automatically interpreting Blast search results.
The oligos designed can be Blast searched, to verify their specificity.
Primer efficiency is enhanced by automatically avoiding template secondary structures.
