Using AlleleID®, you can design assays for identifying species and strains from a mix of sequences
The field of disease diagnosis and drug development has seen a rapid replacement of culture based methods for bacterial and species identification by faster and more reliable molecular based techniques such as real time PCR and microarrays. The reason for the success for these techniques is the ease with which one can identify a species from a sample collected from complex sources such as air, soil, or water.
Molecular based techniques use species-specific probes, designed for specific regions of the target gene, for the detection and identification of bacteria. Microarrays can rapidly detect and identify multiple pathogens simultaneously in complex backgrounds.
AlleleID® designs both real time PCR assays, including molecular beacons, TaqMan® probes, TaqMan® MGB, and SYBR® Green primers), and microarrays for bacterial identification, pathogen detection and taxa/species identification. AlleleID® uses the fast and accurate ClustalW algorithm to align sequences to identify the species specific regions.
Species Identification: Align sequences and identify unique regions
Species Identification: Unique Probes with Unique Primers
Species Identification: Minimal Set with Unique Primers
A "Minimal Probe" Matrix
Y stands for the sequences that can be identified uniquely.
For Optimal, the program minimizes the number of primers required to amplify all sequences. The goal is to minimize the synthesis and overall assay costs.
Species Identification: Minimal probes with Optimal primers
AlleleID® aligns sequences using ClustalW and analyzes conserved and species specific regions. You can then use the program for real time PCR primer design (SYBR® Green primer design included) and dual labeled probe design (TaqMan® probes, TaqMan® MGB probes and molecular beacons). These assays are designed to detect only the strain (strain detection) or species of interest from the mix.
Highly specific oligos are designed by avoiding regions of significant homologies found by automatically interpreting BLAST search results. Real time PCR primer & probe efficiency is enhanced by avoiding template secondary structures. "Minimal Set", one of the most innovative features in the program, helps design the fewest number of allele specific oligonucleotide primers and dual labeled 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, proven set of primers, AlleleID® can design compatible primers and probes for the rest of sequences for species identification or taxa specific assays.