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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

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Maintainer


  • person_outline Jean-Marie Rouillard <>

Publications for OligoArray

OligoArray in pipelines

 (3)
2013
PMCID: 3610128
PMID: 23497009
DOI: 10.1186/1471-2164-14-169

[…] 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 […]

2009
PMCID: 2790472
PMID: 19930683
DOI: 10.1186/1471-2164-10-555

[…] singletons not assembled by the software, as 13,688 nn singletons were mapping to just 10 genes models (data not shown). the number of unigenes in the nn library was therefore overestimated, but the oligoarray software successfully recognized their redundancy. the probe design on the 29,627 n unigenes produced 29,393 specific oligonucleotide sequences (table ). by comparison, the probe design […]

2008
PMCID: 2533675
PMID: 18713468
DOI: 10.1186/1471-2164-9-390

[…] were repeated against the swissprot/trembl [] database. a perl script was developed to summarize and compare the blast results., oligos for the ppav1 sequences were designed with the program oligoarray 2.1 [] to match the melting temperature distribution of agilent's s. cerevisiae oligos on the yeast oligo microarray (v2), design number 013384., the oligo-set for the ppav2 sequence set […]


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OligoArray in publications

 (20)
PMCID: 4026244
PMID: 24841151
DOI: 10.1371/journal.pone.0096876

[…] analyzed as described above. according to rna quality and quantity, the four best samples per strain were chosen for transcriptomic analysis., oligonucleotide microarrays were designed using the oligoarray 2.0 software and produced by agilent. they contain 3,552 gene sequences in the form of oligonucleotides of 45 to 60 nucleotides in length. each gene is mainly represented by two […]

PMCID: 3750854
PMID: 23937585
DOI: 10.1186/1471-2164-14-540

[…] only 18% of the 6,296 torubamubiga unigenes had no hits, indicating that our torvum transcript tags catalogue is likely to represent the most complete dataset for torvum available to date., oligoarray 2.1 software [] was used to compute gene-specific oligonucleotides corresponding to torvum unigenes. oligoarray output, besides microarray design, provides hints on the quality (e.g. […]

PMCID: 3637634
PMID: 23586779
DOI: 10.1186/1471-2164-14-252

[…] instructions. the microarray contains 12889 45-60mer oligonucleotides designed on the predicted gene sequences of strains nem316, a909 and coh1. the oligonucleotide design was carried out with the oligoarray server [] (http://berry.engin.umich.edu/oligoarray/). the microarray was manufactured by agilent technologies. only probes with 100% identity to a909, cf00173, 2-22 and ss1219 sequences […]

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

[…] 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 […]

PMCID: 3510511
PMID: 22989714
DOI: 10.1093/nar/gks864

[…] accession number gse35152., the c. difficile strain 630 genome was obtained from the european molecular biology laboratory (embl) database. probe design for the microarray was performed by using oligoarray 2.0 software (). one to three oligonucleotides were designed for each 3774 intergenic region, including 100 bp of the 3′ and 5′ ends of genes edge. we could not design oligonucleotides […]


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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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