ArticleNucleic acids research2009
An evaluation of custom microarray applications: the oligonucleotide design challenge.
Article in Nucleic acids research, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 19 papers.
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Who cites it
19 citing papers in PubMed.
- Functional and population genetic features of copy number variations in two dairy cattle populations.BMC genomics · 2020Article
- Cluster oligonucleotide signatures for rapid identification by sequencing.BMC bioinformatics · 2018Article
- Development of a DNA-based microarray for the detection of zoonotic pathogens in rodent species.Molecular and cellular probes · 2015Article
- Strain/species-specific probe design for microbial identification microarrays.Applied and environmental microbiology · 2013Article
- Physico-chemical foundations underpinning microarray and next-generation sequencing experiments.Nucleic acids research · 2013Review
- The illusion of specific capture: surface and solution studies of suboptimal oligonucleotide hybridization.BMC research notes · 2013Article
- BOND: Basic OligoNucleotide Design.BMC bioinformatics · 2013Article
- Efficiency, error and yield in light-directed maskless synthesis of DNA microarrays.Journal of nanobiotechnology · 2011Article
- UPS 2.0: unique probe selector for probe design and oligonucleotide microarrays at the pangenomic/genomic level.BMC genomics · 2010Article
- Microarray oligonucleotide probe designer (MOPeD): A web service.Open access bioinformatics · 2010Article
- Detecting variants with Metabolic Design, a new software tool to design probes for explorative functional DNA microarray development.BMC bioinformatics · 2010Article
- Integrating heterogeneous sequence information for transcriptome-wide microarray design; a Zebrafish example.BMC research notes · 2010Article
- chipD: a web tool to design oligonucleotide probes for high-density tiling arrays.Nucleic acids research · 2010Article
- A general framework for optimization of probes for gene expression microarray and its application to the fungus Podospora anserina.BMC research notes · 2010Article
- Teolenn: an efficient and customizable workflow to design high-quality probes for microarray experiments.Nucleic acids research · 2010Article
- Shared probe design and existing microarray reanalysis using PICKY.BMC bioinformatics · 2010Article
- Dynamic probe selection for studying microbial transcriptome with high-density genomic tiling microarrays.BMC bioinformatics · 2010Article
- PrimerBank: a resource of human and mouse PCR primer pairs for gene expression detection and quantification.Nucleic acids research · 2010Article
- Custom design and analysis of high-density oligonucleotide bacterial tiling microarrays.PloS one · 2009Article
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Authors and funding
3 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The increase in feature resolution and the availability of multipack formats from microarray providers has opened the way to various custom genomic applications. However, oligonucleotide design and selection remains a bottleneck of the microarray workflow. Several tools are available to perform this work, and choosing the best one is not an easy task, nor are the choices obvious. Here we review the oligonucleotide design field to help users make their choice. We have first performed a comparative evaluation of the available solutions based on a set of criteria including: ease of installation, user-friendly access, the number of parameters and settings available. In a second step, we chose to submit two real cases to a selection of programs. Finally, we used a set of tests for the in silico benchmark of the oligo sets obtained from each type of software. We show that the design software must be selected according to the goal of the scientist, depending on factors such as the organism used, the number of probes required and their localization on the target sequence. The present work provides keys to the choice of the most relevant software, according to the various parameters we tested.
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