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OligoWiz specifications

Information


Unique identifier OMICS_00831
Name OligoWiz
Interface Web user interface
Restrictions to use None
Computer skills Basic
Stability Stable
Maintained Yes

Maintainer


  • person_outline OligoWiz Team

Publications for OligoWiz

OligoWiz citations

 (6)
library_books

HTSFinder: Powerful Pipeline of DNA Signature Discovery by Parallel and Distributed Computing

2016
Evol Bioinform Online
PMCID: 4750899
PMID: 26884678
DOI: 10.4137/EBO.S35545

[…] s algorithm implements a lock-free hash table optimization for counting k-mers up to 31 bases in length.There are other approaches to find signatures or probe sequences, such as PROBESEL, OligoArray, OligoWiz, YODA, PRIMROSE, and ARB-ProbeDesign. All of them are limited to one selected target or single sequence in each run; thus, they are not applicable for large datasets.In practice, despite the […]

call_split

Detection of a Yersinia pestis gene homologue in rodent samples

2016
PeerJ
PMCID: 4991868
PMID: 27602258
DOI: 10.7717/peerj.2216
call_split See protocol

[…] equence of the pPCP1 plasmid of the Y. pestis genome (CP000310.1) was obtained from the NCBI database for microarray probe design. Probes were designed using two publicly available software packages: OligoWiz (http://www.cbs.dtu.dk/services/OligoWiz/) and Unique Probe Selector (http://array.iis.sinica.edu.tw/ups/). All probes were checked for suitability using an in silico BLAST analysis. The resu […]

library_books

Seeds for effective oligonucleotide design

2011
BMC Genomics
PMCID: 3128067
PMID: 21627845
DOI: 10.1186/1471-2164-12-280

[…] lification, or DNA microarrays.Many software programs have been written to construct good DNA oligonucleotides, such as ProbeSelect [], PROBESEL [], ProMide [], OligoArray [,], ArrayOligoSelector [], OligoWiz [], ROSO [], GoArrays [], and ProDesign []. One crucial issue in designing good oligonucleotides is to minimize the chance of cross-hybridization. Unsuitable regions are filtered out before c […]

library_books

Evaluating oligonucleotide properties for DNA microarray probe design

2010
Nucleic Acids Res
PMCID: 2887943
PMID: 20236987
DOI: 10.1093/nar/gkq039

[…] Complexity scores were calculated for estimating the degree of common sequence fragments in a given oligonucleotide, as described in the OligoWiz program (). The information content can be calculated by the following equation: where is the number of occurrences of a pattern in the genome, represents the pattern length, and nt is the […]

library_books

An evaluation of custom microarray applications: the oligonucleotide design challenge

2009
Nucleic Acids Res
PMCID: 2665234
PMID: 19208645
DOI: 10.1093/nar/gkp053

[…] m values are ideal to increase sensitivity during the hybridization process (A). When we look at the Tm mean and the interquartile range (IQR), ArrayOligoSelector (Tm mean of 90.94°C, IQR of 1.9) and OligoWiz (Tm mean of 91.09°C, IQR of 2) show the narrowest Tm distribution associated with greater Tm means. OligoFaktory also provides a high Tm mean (97.84°C), but this result must be considered wit […]

library_books

The unique probe selector: a comprehensive web service for probe design and oligonucleotide arrays

2008
BMC Bioinformatics
PMCID: 2259409
PMID: 18315861
DOI: 10.1186/1471-2105-9-S1-S8

[…] nd Picky [] are stand-alone application tools run in command mode and provide unique probes for input sequences under the constrains of GC%, Tm, absence of low complexity and position near the 3'end. OligoWiz2 [] is a java-base server-client solution for probe design in a graphical user interface. Oligodb [] is a database of pre-calculated probes for human and mouse transcriptome. Although most of […]

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OligoWiz institution(s)
Center for Biological Sequence Analysis, Technical University of Denmark, Kgs, Lyngby, Denmark

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