AlleleID 4.01 review

by on

AlleleID is a comprehensive desktop program created to address the challenges of bacterial identification, pathogen detection or taxa/species detection.

License: Demo
OS: Mac OS X
File size: 23952K
Developer: Premier Biosoft
Price: $0.00
Updated: 16 Jan 2007
0 stars award from

AlleleID is a comprehensive desktop program created to address the challenges of bacterial identification, pathogen detection or taxa/species detection. With ClustalW multiple sequence alignment at its core, AlleleID can be used to design species detection/cross species probes for microarrays or real time PCR including SYBR Green, TaqMan MGB, TaqMan probes, Molecular Beacons and real time PCR primers. AlleleID also offers support for designing microarray experiments for detecting alternative splicing events.

Species Detection Assays/Cross Species Assays/Allele identification Assays

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 or species of interest from the mix.

For cross species assays, AlleleID identifies the conserved regions to design a universal probe. For related organisms, AlleleID can be used to study gene expression when genome draft of the organism under study is not available. This powerful functionality is sure be helpful for many challenging tasks such as detection, identification, quantification or monitoring of contaminants, environments...

Sophisticated Algorithms for Assay Success

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 identified by connecting to the Mfold server.

"Minimal Set", one of the most innovative features in the program, helps design the fewest number of allele specific oligonucleotides (real time PCR 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 detection or taxa specific assays.

Extensive support for real time or quantitative PCR Assays & SNP/expression microarrays

AlleleID designs optimal SYBR Green primers, TaqMan® probes, TaqMan® Minor Groove Binding (MGB) probes, FRET probes or molecular beacons for real time quantitative PCR differential gene expression and SNP genotyping assays. You can also design real time PCR primers and dual labeled probes for up to ten thousand sequences in a single run for making SNP detection or expression microarrays.

Here are some key features of "AlleleID":
Real Time PCR Primer Design
SYBR Green Primer Design
TaqMan Probe Design
Molecular Beacon Design
FRET probe design
Microarray Probe Design
Database Support
Input & Output Formats

AlleleID 4.01 keywords