AlleleID

AlleleID Publisher's Description:
AlleleID is a comprehensive desktop tool designed to address the challenges of pathogen detection, bacterial identification or taxa/species discrimination using microarrays and TaqMan® and molecular beacon qPCR assays. With ClustalW multiple sequence alignment at its core, AlleleID can design species specific/cross species probes for microarrays or TaqMan®/molecular beacon qPCR assays. You could use both the techniques; verify microarray results using qPCR, or perhaps, make microarrays based on probes through qPCR.

WHAT'S NEW

Version 5.0:

* MLPA® Assays- With AlleleID 5.00, you can design highly specific probes for MLPA® assays. MLPA, short for Multiplex ligation-dependent probe amplification is popularly used for detection of amplifications and deletions in a variety of genes. Using AlleleID you can design MLPA® probes, both for copy number detection and mutation studies.
* Use Pre-designed Probes- For published or pre-designed probes, AlleleID now designs compatible primers and completes your species or taxa specific assays.
* Design Degenerate Primers- You can even design degenerate or mismatch tolerant primers for taxa assays where conservancy is disturbed due to presence of mismatches.
* Multiplex TaqMan® more...Assays- AlleleID now includes comprehensive support for multiplexing. The program is now equipped with innovative proprietary algorithms to design the most optimal primer-probe sets for multiplex reactions. The sets are chosen by minimizing Tm mismatches and cross dimerization and are made available in a sortable list. For multiplex assays, you can even design oligos for additional sequences that are compatible with the pre-designed sets for certain sequences. This feature may be most useful for incorporating a well-proven reference or housekeeping gene in a reaction. It is also possible to check the suitability of pre-designed primer sets for a multiplex reaction.
* Batch BLAST and Template Structure Search- You can now perform BLAST and template structure search for multiple sequences in a single search run.