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Probe design software tools | Fluorescence in situ hybridization

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…
HD FISH
Desktop

HD FISH High-Definition DNA FISH

Allows high-definition of DNA fluorescence in situ hybridization (FISH). HD…

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…

OligoArray
Desktop

OligoArray

A free software that computes gene specific oligonucleotides for genome-scale…

A free software that computes gene specific oligonucleotides for genome-scale oligonucleotide microarray construction.

probeBase
Dataset

probeBase

A manually maintained and curated database of rRNA-targeted oligonucleotide…

A manually maintained and curated database of rRNA-targeted oligonucleotide probes and primers. Contextual information and multiple options for evaluating in silico hybridization performance against…

PROBER
Desktop

PROBER

Produces Tiling Oligonucleotide Probes (TOPs), as alternatives to bacterial…

Produces Tiling Oligonucleotide Probes (TOPs), as alternatives to bacterial artificial chromosomes (BACs). PROBER masks repetitive genomic sequences and delineates essentially unique regions that can…

Kmasker
Web

Kmasker

Serves for in silico extraction of unique genomic sequence information. Kmasker…

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…

OligoMiner
Desktop

OligoMiner

Permits oligo hybridization probes. OligoMiner employs supervised machine…

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…

ProbeMaker
Desktop

ProbeMaker

A Java software project aimed at providing a framework for design and analysis…

A Java software project aimed at providing a framework for design and analysis of sets of oligonucleotide probes for use in multiplex assays for nucleic acid analyses and other purposes.

webFISH
Web

webFISH

Recognizes all potential specific single-copy and/ or repetitive Fluorescence…

Recognizes all potential specific single-copy and/ or repetitive Fluorescence in-situ hybridization (FISH) probes inside a user-specified chromosomal sequence. webFISH can design FISH probes for…

mathFISH
Web
Desktop

mathFISH

Offers the users up-to-date knowledge of hybridization thermodynamics within a…

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.…

H-MAPD
Web

H-MAPD

Automates the design of multiplex ligation-dependent probe amplification (MLPA)…

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…

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