Oligonucleotide design software tools | Microarray data analysis

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 to probe selection according to a series of probe quality parameters, cross-hybridization, T(m), position in transcript, probe folding and low-complexity, the program facilitates automatic placement of probes relative to the sequence annotation. The program also supports automatic placement of multiple probes per transcript. Together these facilities make advanced probe design feasible for scientists inexperienced in computerized information management.

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.

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.

Integrates a probe quality score calculation. Teolenn is a flexible and universal probe design solution based on an open module system approach. It works as a four-step workflow and it probes: (i) library creation, (ii) parameter calculation, (iii) filtering and (iv) selection. It also assigns a quality score to each designed probe so that a posteriori filtering steps and correlations can be made.

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.

Allows computation or retrieval of redefined Affymetrix probe sets. AffyProbeMiner uses mRNA RefSeqs and validated complete coding sequences in GenBank to (1) regroup the individual probes into consistent probe sets and (2) remap the probe sets to the correct sets of mRNA transcripts. It was used to study several biologically and biomedically important research problems, including enhanced characterization of the NCI-60 cancer cell line. The command-line code allows the user to generate the altered mapping files.

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 perfect duplications. This tool can be applied for oligonucleotide design in order to solve the problem of specificity in a complex biological system retaining a high sensitivity for long oligonucleotides.

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 and shared words, which are found with the spaced seed hashing algorithm. To detect more sequences, those sharing some common words are re-clustered into new families, then probes specific for the new families are generated. ProDesign is very flexible in that it can be used for designing probes for detecting many genes families simultaneously and specifically in one or more genomes. Neither the length nor the melting temperature of the probes needs to be predefined. The program provides biologists with a powerful tool for an easy, rapid and flexible design of oligonucleotide probes for environmental microarrays and related applications.

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 as input a target sequence set and a database of non-target sequences.

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 crucial problem of cross-hybridizations, probe specificity is assessed by similarity search against a large formatted database dedicated to microbial communities containing about 10 million coding sequences (CDS).

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 for each target taxon.

Designs selector probes for exon resequencing of a set of genes. Disperse is an integrated software system that generates a set of selector probe sequences, designed to select the largest possible portion of the targeted sequence. The software performs the design work in a pipeline fashion, where several steps are executed sequentially. Disperse depends on external data sources, programs and libraries.

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

Facilitates bait development for an array of molecular applications. MrBait is a flexible software that stores genomic regions or alignments, candidate target regions, and candidate probe sequences as an SQLite relational-database. It can be generalized to any targeted-enrichment paradigm. It simultaneously identifies conservative ‘target’ regions in user-provided sequence data, designs probes to enrich them, and curates the resulting bait set.

Analyzes next-generation sequencing (NGS) from experiments using unique molecular identifiers (UMI) and for setting data for downstream analysis. AmpUMI permits the evaluation of the quality of UMIs and figures out if the UMI pool have adequate diversity to avoid UMI collisions. This software features trimming of the UMI and offers to users an adapter sequence to adapt the tool to a specific UMI and sequencing design.

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 > 10% typically) and subsequently clusters both controls and cases to discover a structure that may separate controls from cases.

Represents a genome-aware primer pair design algorithm. ThermoAlign is able to use prior information on the locations of genomic variants during the selection of primer pairs. In order to design primer pairs forming amplicon tiling paths, a directed graph analysis method is used by this tool. It simplifies targeted genome sequence studies for any species.

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 custom-built mRNA reference database to identify the positions of gene expression array probe sequences.

Creates custom expression microarrays (CEMs) for complex transcriptomes. CEM-designer is a web application that is composed of two main features: (i) the first characteristic allows users to provide unified target sequences suitable for an external software to design probe; (ii) the second feature authorizes to summarize statistics and to estimate probe specificity from both a submission or a personal file.

Investigates and selects oligos from unigenes sequences. OligoSpawn is composed of three main panels: (i) popular oligo design, that allows users to pick oligo from sequences; (ii) popular oligo check, that depicts correspondence between popular oligos and sequences; and (iii) unique oligo design, that detects oligos that are unique into sequences. The web application can perform only files of 50 megabases and less. To perform larger files, users have to install the desktop version of the software.

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.

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 metabolic pathways in complex environments, and it may also be used to study any group of genes.

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 facilitates large scale multiplex assays, without Polymerase chain reaction (PCR) sample preparation and select highly unique probes specific for each target sequence.

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

Designs multiplex polymerase chain reaction (PCR) experiments suitable for next-generation targeted resequencing. MPD allows an iterative design approach where initially stringent conditions and subsequently loosened to maximize the number of high-quality primers that are as close to the initial design criteria as biologically feasible. This application can be quickly retooled to enable shift in targeted genes as new genetic evidence emerges.

Assists in the design of a pan-genome CGH tiling array for Listeria monocytogenes. PanArray is implemented for pan-genome tiling array construction that both reduces the number of probes required and guarantees that all sequences in the pangenome are fully tiled by the array. It can be applied to seven different bacterial pan-genomes. This tool provides flexibility for the analysis, detection, or capture of genomic material for entire species.

Allows design of TAC-seq probes. TAC-seq probe design automates probe design procedure and provides highly specific oligonucleotide sequences with common motifs that are ready for synthesizing.

Assists users in designing probes. PhylGrid allows selecting both specific and explorative (discovery of possible new species) probes with respect to sensitivity and specificity. This method was used to create a complete phylogenetic oligonucleotide database composed of about 20,000 probes targeting 2,069 prokaryotic genera. It also allows users to submit parallel jobs to the European Computing Grid Infrastructure (EGI) computing grid from Biomed Virtual Organization.

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

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 probes. It can verify the specificity, the number of cross-hybridization, the Tm, the GC content, the possible secondary structures formed and the existence of homopolymers for each potential probe. This tool can assist in identification of new organisms or variant genes.

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

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

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 two groups of nucleic-acid sequences, a target group and a non-target group, the software identifies oligo sequences that occur in members of the target group, but not in the non-target group. To help predict potential cross hybridization, PROBEmer computes all near neighbors in the non-target group and displays their alignments. Because it does not rely upon multi-alignments, it can be applied to sequences which are not similar (e.g. genes in a single organism) or to variations of a gene in many organisms (e.g. 16S rRNA gene).

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

Assists users in the design of microarray probe sets. YODA can design one or multiple oligo probes per sequence with the possibility to customize the parameters such as, among others, oligo length, maximum percent identity with a non-target sequence or melting temperature range. This software supports three classes of DNA sequence files (design, genome and host) to achieve multiple design strategies.

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

Allows users to input and analyse microarray data from the Xspecies microarray approach. Pigeons employs quantile normalization to address the comparability of intensity distributions between arrays. It is focused around visualization and interactive studies of the datasets at the probe level. It also provides a specific visualization interface to facilitate navigation through the hundreds of thousands of Affymetrix oligonucleotides.