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HD FISH / High-Definition DNA FISH
Allows high-definition of DNA fluorescence in situ hybridization (FISH). HD FISH can operate at the resolution limit of conventional optical microscopy due to the systematic design of unique probes with short span. It enables visualization of virtually any human or mouse genomic locus. This tool allows users to fully exploit the potential of DNA FISH. It provides human and mouse genomic libraries of polymerase chain reaction (PCR) primer pairs with optimal thermodynamic features.
Designs specific oligonucleotides at the genomic scale. OligoArray computes gene-specific and secondary structure-free oligonucleotides for genome-scale oligonucleotide microarray construction. This program also uses the Lempel-Ziv (LZ) sequence complexity criteria, and allows the design of oligonucleotides for use on microarrays for gene expression profiling. It can manage neither polymorphism nor splicing variants, except by considering each variant as a different input sequence.
Automates the design of multiplex ligation-dependent probe amplification (MLPA) copy number assays. H-MAPD can be applied to human genomic MLPA probe design and be generalized to other genomes. It allows users to employ their own stuffer sequences or bead tag sequences and to specify custom polymerase chain reaction (PCR) primers. This tool can deal with the design of MLPA assays for other applications, such as single nucleotide polymorphism (SNP) detection and methylation changes.
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