Probe Design: You can design MLPA® probes, both for copy number detection and SNP studies. The software was developed in collaboration with MRC Holland, the inventors of the technology, and follows all MLPA design guidelines. AlleleID® can also design custom oligos for Pam4U PamChip® Arrays.
Avoid Homology: AlleleID® designs highly specific MLPA®probes by automatically avoiding the regions of homology identified during a BLAST search.
Multiplex MLPA® Probes: Displays the free energies of the most stable cross-dimers formed between the MLPA® probes, helping you determine which probes are best suited for a multiplex reaction.
Load SNPs: Easily loads sequences containing SNPs from the variation descriptors in standard GenBank variation files and from UCSC file. If you are working with unpublished data you can easily add them.
Load Exons: Retrieves exon information from GenBank header annotations and UCSC genome browser. If you are working with unpublished data you can easily add them.
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.