ArticleBMC bioinformatics2013
BOND: Basic OligoNucleotide Design.
Article in BMC bioinformatics, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 7 papers.
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Who cites it
7 citing papers in PubMed.
- Probe design for simultaneous, targeted capture of diverse metagenomic targets.Cell reports methods · 2021Article
- AnthOligo: automating the design of oligonucleotides for capture/enrichment technologies.Bioinformatics (Oxford, England) · 2020Article
- Mismatch-tolerant, alignment-free sequence classification using multiple spaced seeds and multiindex Bloom filters.Proceedings of the National Academy of Sciences of the United States of America · 2020Article
- Cluster oligonucleotide signatures for rapid identification by sequencing.BMC bioinformatics · 2018Article
- Oli2go: an automated multiplex oligonucleotide design tool.Nucleic acids research · 2018Article
- Best hits of 11110110111: model-free selection and parameter-free sensitivity calculation of spaced seeds.Algorithms for molecular biology : AMB · 2017Article
- A coverage criterion for spaced seeds and its applications to support vector machine string kernels and k-mer distances.Journal of computational biology : a journal of computational molecular cell biology · 2014Article
Corrections and comments
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Authors and funding
4 authors.
Funding
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Abstract
backgroundDNA 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 the highest possible number of genes, that is, all genes that allow such unique regions, and (iii) are computed fast. None of the existing programs meet all these criteria.
resultsWe introduce a new approach with our software program BOND (Basic OligoNucleotide Design). According to Kane's criteria for oligo design, BOND computes highly specific DNA oligonucleotides, for all the genes that admit unique probes, while running orders of magnitude faster than the existing programs. The same approach enables us to introduce also an evaluation procedure that correctly measures the quality of the oligonucleotides. Extensive comparison is performed to prove our claims. BOND is flexible, easy to use, requires no additional software, and is freely available for non-commercial use from http://www.csd.uwo.ca/∼ilie/BOND/.
conclusionsWe provide an improved solution to the important problem of oligonucleotide design, including a thorough evaluation of oligo design programs. We hope BOND will become a useful tool for researchers in biological and medical sciences by making the microarray procedures faster and more accurate.
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Registered trials
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