In the News..15-11-2006 CLC bio New Hardware Accelerator CLCbio have created the CUBE. A hardware unit which runs Smith Waterman up to 125 times faster than a 3 GHz desktop computer. Using the Cube instead of BLAST, improves the quality of the data you're working with! read more.. |
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AlleleID FeaturesSpecies Detection Assays/Cross Species Assays/Allele identification AssaysAlleleID aligns sequences using ClustalW and analyzes conserved and species specific regions. You can then use the program for real time PCR primer design (SYBRŽ Green primer design included) and dual labeled probe design (TaqManŽ probes, TaqManŽ 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 SuccessHighly 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 microarraysAlleleID designs optimal SYBRŽ Green primers, TaqManŽ probes, TaqManŽ 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. Features summary
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