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OligoArray specifications

Information


Unique identifier OMICS_00828
Name OligoArray
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Programming languages Java
Computer skills Advanced
Version 2.1
Stability Stable
Registration required Yes
Maintained Yes

Versioning


No version available

Maintainer


  • person_outline Jean-Marie Rouillard

Publications for OligoArray

OligoArray citations

 (9)
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

[…] arallel. This 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, […]

library_books

Transcriptome analysis of pigeon milk production – role of cornification and triglyceride synthesis genes

2013
BMC Genomics
PMCID: 3610128
PMID: 23497009
DOI: 10.1186/1471-2164-14-169

[…] ions were combined (430654) and assembled with Newbler v2.3 shotgun assembler (Roche). The resulting contigs (10463) and remaining Singletons (71997) were used to design unique microarray probes with OligoArray 2.1 []. The microarray probes were annotated via the source contigs or read sequences by a series of BLAST searches using an E-value of 10-3 as cut-off for all searches. The first search us […]

library_books

Seeds for effective oligonucleotide design

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

[…] on, PCR (polymerase chain reaction) amplification, 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. Unsui […]

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

[…] and all oligo sets fit in this range except for OligoFaktory (63.9%). Sensitivity can also be adjusted by adapting the oligonucleotide size to fit within the Tm and GC percent set up by the software. OligoArray, OligoPicker, ArrayOligoSelector, ROSO, YODA, CommOligo and Mprime design all the oligonucleotides with the same size (50 bp). The other software programs adapt the oligonucleotide size to […]

library_books

Expressed sequence tags (ESTs) from immune tissues of turbot (Scophthalmus maximus) challenged with pathogens

2008
PMCID: 2569028
PMID: 18817567
DOI: 10.1186/1746-6148-4-37

[…] based on annotations, to perform local BLAST searches, and to select sequences for a prospective microarray were also included. These tools used RepeatMasker for masking low-complexity sequences and OligoArray 2.1 to predict secondary structures and potential cross-hybridization.As shown in Table , 1716 (49.3%) unique sequences displayed no significant similarity to known sequences or ESTs in th […]

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

[…] ich can form binding pairs in the reaction.Several tools are available for probe design. Most of these are performed in command mode, and only few provide a Graphic User Interface (GUI). For example, OligoArray 2.1 [,], GoArrays [], OligoPicker [], ArrayOligoSelector [] and Picky [] are stand-alone application tools run in command mode and provide unique probes for input sequences under the constr […]

Citations

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OligoArray institution(s)
Department of Chemical Engineering, University of Michigan, Ann Arbor, MI, USA; Department of Mathematical Sciences, Rensselaer Polytechnic Institute, Troy, NY, USA
OligoArray funding source(s)
Supported by the Michigan Life Sciences Corridor funding grant no. MEDC-GR171, DARPA contract no. N39998-01-C-7071 (Xeotron Prime Contractor) and by a grant from NIH, no. GM54250.

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