Using AlleleID®, you can design assays for identifying species and strains from a mix of sequences
- Specifying Sequences: Specify the sequences you would like to detect in the mix by moving them to the "Bind To" box.
- Choices for Primer Design: There are two choices available for primer design, Unique and Optimal. When you choose Unique, the program designs a primer pair to amplify each sequence. 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.
- Choices for Probe Design: Similarly for probes, when you choose Unique, AlleleID® designs one probe per sequence. When you choose the Minimal
set option, AlleleID® designs the smallest number of probes required to identify the sequences.
How Species Were Identified Historically
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.
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
Modern Techniques for Species Identification
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
Identification: Align sequences and identify unique regions
AlleleID® Provides a Number of Options for Species Identification
Probes with Unique Primers:
the probe type chosen is Unique, AlleleID® designs probes to
identify each sequence in the Bind To box, one probe per
sequence. The program
searches for base positions that are unique to each individual
sequence in the alignment. The probes are centered as close as
possible over these unique bases, so that even when the mismatch is
only one base, the assay succeeds.
Identification: Unique Probes with Unique Primers
Set with Unique Primers: Choosing the Minimal set option, AlleleID® designs the smallest number of
probes required to identify the sequences. The Minimal set will
generally contain fewer probes than the number of sequences to be
identified, and a unique combination of probes identifies each
sequence. The aim of such an assay is to minimize the
synthesis and overall assay costs.
Identification: Minimal Set with Unique Primers
"Minimal Probe" Matrix
stands for the sequences that can be identified uniquely.
Identification: Minimal probes with Optimal primers