Though a formidable portfolio of ready-to-use probes is available from various commercial sources, the choice is usually restricted to a relatively small number (<200) of loci mostly belonging to the human genome. Probes targeting other loci or species can be developed from genomic DNA fragments cloned in bacterial artificial chromosomes (BACs) and fosmids, or using array-based technology. However, implementing these methods in-house or outsourcing them to commercial parties can be challenging if not impossible for many laboratories for both logistic and economic reasons.
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.
Combines several steps for a high-quality probe and primer design for a variety of biological experiments. Oli2go is a web application designed to manage more than one sequence for multiplex reactions. Moreover, it can support sequences containing ambiguous nucleotides but should be used carefully as each variable position within the sequence increases the number of computational steps.
Permits oligo hybridization probes. OligoMiner employs supervised machine learning to predict thermodynamic behavior from genome-scale sequence alignment information. It can be applied on any sequenced genome and can mine the entirety of the human genome in minutes to hours. This tool can be used to design hybridization probes for a wide range of experimental assays beyond in situ hybridization.
Produces Tiling Oligonucleotide Probes (TOPs), as alternatives to bacterial artificial chromosomes (BACs). PROBER masks repetitive genomic sequences and delineates essentially unique regions that can be amplified to yield small DNA probes. This tool can only be applied if targeted locus contains at least 10kb of essentially unique blocks.
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