This software aims to overcome issues in identifying bacteria, detecting pathogens, and determining taxa/species, by addressing their challenges.
AlleleID is a versatile desktop program that has been designed to tackle the challenges of bacterial identification, pathogen detection, or taxa/species detection. At its core, AlleleID utilizes ClustalW multiple sequence alignment to create species detection or cross-species probes for microarrays or real-time PCR, including SYBR Green, TaqMan MGB, TaqMan probes, molecular beacons, and real-time PCR primers. Additionally, the program also provides support for designing microarray experiments to detect alternative splicing events.
AlleleID functions by aligning sequences with ClustalW and analyzing both conserved and species-specific regions, allowing users to design highly specific oligos that identify only the desired strain or species from a mix. For cross-species assays, AlleleID identifies the conserved regions to design a universal probe. Furthermore, the program can be used to study gene expression in related organisms when a genome draft is not available.
AlleleID incorporates sophisticated algorithms to enhance the efficiency of real-time PCR primers and probes by avoiding regions of significant homology and identifying template secondary structures via connection to the Mfold server. "Minimal Set," an innovative feature of the program, helps users design the fewest number of allele-specific oligonucleotides (real-time PCR primers and dual-labeled probes) necessary to uniquely identify each desired species/strain/taxon from the mix, thereby reducing assay costs.
The program also offers extensive support for real-time or quantitative PCR assays and SNP/expression microarrays with optimal design for SYBR Green primers, TaqMan probes, TaqMan MGB probes, FRET probes, or molecular beacons. Finally, users can 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. Overall, AlleleID is a comprehensive program that provides powerful functionality to tackle complex tasks such as detection, identification, quantification, or monitoring of contaminants and environments.
AlleleID functions by aligning sequences with ClustalW and analyzing both conserved and species-specific regions, allowing users to design highly specific oligos that identify only the desired strain or species from a mix. For cross-species assays, AlleleID identifies the conserved regions to design a universal probe. Furthermore, the program can be used to study gene expression in related organisms when a genome draft is not available.
AlleleID incorporates sophisticated algorithms to enhance the efficiency of real-time PCR primers and probes by avoiding regions of significant homology and identifying template secondary structures via connection to the Mfold server. "Minimal Set," an innovative feature of the program, helps users design the fewest number of allele-specific oligonucleotides (real-time PCR primers and dual-labeled probes) necessary to uniquely identify each desired species/strain/taxon from the mix, thereby reducing assay costs.
The program also offers extensive support for real-time or quantitative PCR assays and SNP/expression microarrays with optimal design for SYBR Green primers, TaqMan probes, TaqMan MGB probes, FRET probes, or molecular beacons. Finally, users can 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. Overall, AlleleID is a comprehensive program that provides powerful functionality to tackle complex tasks such as detection, identification, quantification, or monitoring of contaminants and environments.
What's New
Version 7.5: N/A