Generate Report: You can create an attractively formatted report for the assays you designed using AlleleID®. It should be helpful in record keeping and for sharing information with colleagues. The report helps visualize the positions of the primers and probes on the sequence, includes a list of the alternate primers and probes, displays primers, probe, amplicon and sequence properties and the design parameters used.
Sequence Details View: Comprehensive information of all sequences in a project is available locally using the built-in database and the sequence details can be viewed using your browser from within the program.
Sequence Visualization: AlleleID® graphically displays the primers and probes on the sequence.
Input Formats: Supports sequences in standard GenBank and FASTA format. Using the multiple retrieval facility, sequences can be loaded from local drives.
SNP Loading: Easily loads thousands of SNPs from the variation descriptors in standard GenBank variation files.
View Output in Spreadsheet: Results can be viewed and manipulated in any spreadsheet like MS Excel, Lotus 123 or StarOffice spreadsheet.
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.