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Oligonucleotide design software tools | Microarray data analysis

DNA microarrays have become ubiquitous in biological and medical research. The most difficult problem that needs to be solved is the design of DNA oligonucleotides that (i) are highly specific, that is, bind only to the intended target, (ii) cover…
OligoWiz
Web

OligoWiz

A powerful tool for microarray probe design that allows for integration of…

A powerful tool for microarray probe design that allows for integration of sequence annotation, such as exon/intron structure, untranslated regions (UTRs), transcription start site, etc. In addition…

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.

Osprey
Desktop

Osprey

Calculates optimal oligonucleotides for a range of tasks: sequence assembly,…

Calculates optimal oligonucleotides for a range of tasks: sequence assembly, differential expression, and microarrays (cDNA and spotted oligos).

OligoArrayDb
Dataset

OligoArrayDb Pangenomic Oligonucleotide Microarray Probe Sets Database

Gathers oligonucleotide microarray probe sequences, including those not covered…

Gathers oligonucleotide microarray probe sequences, including those not covered by commercial catalog arrays. OligoArrayDB intends to provide tools for any transcriptome analysis on sequenced…

ProDesign
Web

ProDesign

A tool developed for the selection of oligonucleotide probes to detect members…

A tool developed for the selection of oligonucleotide probes to detect members of gene families present in environmental samples. Gene family-specific probe sequences are generated based on specific…

OligoFaktory
Desktop

OligoFaktory

A free software for Mac OS X which designs long oligos for DNA microarrays,…

A free software for Mac OS X which designs long oligos for DNA microarrays, primers for PCR, siRNAs, and more…

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.

Re-Annotator
Desktop

Re-Annotator

A re-annotation pipeline for microarray probe sequences. The Re-Annotator is…

A re-annotation pipeline for microarray probe sequences. The Re-Annotator is primarily designed for gene expression microarrays but can also be adapted to other types of microarrays. It uses a…

Picky software
Desktop

Picky software

Allows the rapid and efficient determination of gene-specific oligos based on…

Allows the rapid and efficient determination of gene-specific oligos based on given gene sets, and can be used for large, complex genomes such as human, mouse, or maize.

ProbeSelect
Desktop

ProbeSelect

A statistical formalism for selection of the probes that distinguish…

A statistical formalism for selection of the probes that distinguish heterogeneous disease samples from healthy controls. ProbeSelect considers all probes with a high coefficient of variation (CV…

PathogenMIPer
Desktop

PathogenMIPer

Allows users to create molecular inversion probes (MIP). PathogenMIPer is a…

Allows users to create molecular inversion probes (MIP). PathogenMIPer is a standalone tool which aims to improve multiple target DNAs detection in a sample by easing MIP assays development. It…

BOND
Desktop

BOND Basic OligoNucleotide Design

Computes highly specific DNA oligonucleotides, for all the genes that admit…

Computes highly specific DNA oligonucleotides, for all the genes that admit unique probes, while running orders of magnitude faster than the existing programs.

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celegansprobe
Dataset

celegansprobe

Probes sequence for microarrays of type celegans. celegansprobe is an R package…

Probes sequence for microarrays of type celegans. celegansprobe is an R package available on Bioconductor.

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canineprobe
Dataset

canineprobe

Probes sequence for microarrays of type canine2. canineprobe is an R package…

Probes sequence for microarrays of type canine2. canineprobe is an R package available on Bioconductor.

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bsubtilisprobe
Dataset

bsubtilisprobe

Probes sequence for microarrays of type bsubtilis. bsubtilisprobe is a module…

Probes sequence for microarrays of type bsubtilis. bsubtilisprobe is a module created by the package AnnotationForge.

FDb.InfiniumMet…
Dataset

FDb.InfiniumMethylation.hg

Offers a compilation of HumanMethylation27 and HumanMethylation450 annotations.

Offers a compilation of HumanMethylation27 and HumanMethylation450 annotations.

ecoliprobe
Dataset

ecoliprobe

Provides probe sequence for microarrays of type Escherichia coli. ecoliprobe…

Provides probe sequence for microarrays of type Escherichia coli. ecoliprobe was automatically constructed by the AnnotationForge package.

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drosophilaprobe
Dataset

drosophilaprobe

Gathers information on sequences for microarrays related to insect…

Gathers information on sequences for microarrays related to insect (drosophila). The drosophilaprobe data are generated by the package AnnotationForge.

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cottonprobe
Dataset

cottonprobe

Gathers information on sequences for microarrays related to cotton. The…

Gathers information on sequences for microarrays related to cotton. The cottonprobe data are generated by the package AnnotationForge.

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chickenprobe
Dataset

chickenprobe

Gathers information on sequences for microarrays related to chicken. The…

Gathers information on sequences for microarrays related to chicken. The chickenprobe data are generated by the package AnnotationForge.

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bovineprobe
Dataset

bovineprobe

Furnishes a R package gathering probe sequence for microarrays of bovine.…

Furnishes a R package gathering probe sequence for microarrays of bovine. bovineprobe provides information such as x et y coordinate on the array or probe interrogation position.

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barley1probe
Dataset

barley1probe

Provides a R package that constitutes a repository containing probe sequence…

Provides a R package that constitutes a repository containing probe sequence for microarrays of barley1. barley1probe furnishes information on probe sequence, its x et y coordinate on the array, the…

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ath1121501probe
Dataset

ath1121501probe

Provides a repository of probes from Arabidopsis thaliana generated by…

Provides a repository of probes from Arabidopsis thaliana generated by AnnotationForge. Ath1121501probe includes information about probe sequence, its x et y coordinate on the array, the Affymetrix…

agprobe
Dataset

agprobe

Provides a R package containing a repository composed of probes sequences…

Provides a R package containing a repository composed of probes sequences related to Arabidopsis thaliana.

KASpOD
Desktop
Web

KASpOD K-mer based algorithm for high specific oligonucleotide design

A web service dedicated to the design of signature sequences. Highly specific…

A web service dedicated to the design of signature sequences. Highly specific selected oligonucleotides are suitable for various goals including phylogenetic or functional microarrays. KASpOD takes…

HiSpOD
Web

HiSpOD High Specific Oligo Design

A functional microarray probe design algorithm. HiSpOD uses individual nucleic…

A functional microarray probe design algorithm. HiSpOD uses individual nucleic sequences or consensus sequences produced by multiple alignments to design highly specific probes. Indeed, to bypass…

PhylArray
Web

PhylArray

A probe design algorithm that is able to select microarray probes targeting SSU…

A probe design algorithm that is able to select microarray probes targeting SSU rRNA at any phylogenetic level. This original approach designs a combination of degenerate and non-degenerate probes…

PhylOPDb
Dataset

PhylOPDb

An online resource for a comprehensive phylogenetic oligonucleotide probe…

An online resource for a comprehensive phylogenetic oligonucleotide probe database. PhylOPDb provides a convivial and easy-to-use web interface to browse both regular and explorative 16S…

OligoPicker
Desktop

OligoPicker

It is to help selecting up to five oligo probes for each of the DNA sequences…

It is to help selecting up to five oligo probes for each of the DNA sequences you provided for microarray spotting.

Metabolic…
Desktop

Metabolic Design

Generates efficient explorative probes using a simple convenient graphical…

Generates efficient explorative probes using a simple convenient graphical interface. Metabolic Design is a powerful, efficient tool that can be used to design explorative probes and monitor…

MetaExploArrays
Desktop

MetaExploArrays

Allows probe design for an individual nucleic acid sequence or a group of…

Allows probe design for an individual nucleic acid sequence or a group of sequences. MetaExploArrays takes into account all significant known criteria to choose sensitive, specific and isothermal…

GoArrays
Desktop

GoArrays

Provides a probe design strategy. GoArrays is based on the determination of two…

Provides a probe design strategy. GoArrays is based on the determination of two specific subsequences. It was able to design specific probes for each coding data sequence (CDS) of the genome except…

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PMPj-Blast
Dataset

PMPj-Blast

Offers data from were obtained from PMPj. PMPj-Blast is a database of…

Offers data from were obtained from PMPj. PMPj-Blast is a database of nucleotide sequences of Expressed Sequence tags (ESTs), cDNAs and oligo DNA microarray probes for Lotus japonicus and Arabidopsis…

Array Designer
Desktop

Array Designer

Designs thousands of primers and probes for oligo and cDNA microarrays in…

Designs thousands of primers and probes for oligo and cDNA microarrays in seconds.

ArrayOligoSelec…
Desktop

ArrayOligoSelector

We have developed a program to systematically design gene specific long…

We have developed a program to systematically design gene specific long oligonucleotide probes for entire genomes, for the purpose of developing whole genome microarrays.

PROBEmer
Web

PROBEmer

A web-based software tool that enables a researcher to select optimal oligos…

A web-based software tool that enables a researcher to select optimal oligos for PCR applications and multiplex detection platforms including oligonucleotide microarrays and bead-based arrays. Given…

ROSO
Desktop

ROSO

Optimized oligonucleotide probes (size over 25 nucleotides) for microarrays.

Optimized oligonucleotide probes (size over 25 nucleotides) for microarrays.

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