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.
Addresses the challenges of bacterial identification, pathogen detection or species identification. AlleleID is a comprehensive desktop tool to design species identification/cross species probes for microarrays or real time polymerase chain reaction (PCR) including SYBR Green, TaqMan MGB, TaqMan probes, Molecular Beacons and real time PCR primers. AlleleID also offers support for designing microarray experiments for detecting alternative splicing events.
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.
Offers the users up-to-date knowledge of hybridization thermodynamics within a theoretical framework. MathFISH is expected to maximize the probability of success during oligonucleotide probe design. This tool calculates all modeled thermodynamic properties of a single probe for any target molecule provided (i.e., perfect match or with mismatches). mathFISH provides thermodynamic estimations for any type of mismatch, including bulged mismatches, and combinations of mismatches.
Serves for in silico extraction of unique genomic sequence information. Kmasker is a program allowing detection of high-quality candidates that are unique or occur at very low frequency in the genome. It can be used for the integration of genetic and cytogenetic maps in large and complex plant genomes.
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.
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.