OligoArray: genome-scale oligonucleotide design for microarrays

Rouillard, Jean Marie; Herbert, Christopher J.; Zuker, Michael

doi:10.1093/bioinformatics/18.3.486

Cited by 148 publications

(97 citation statements)

References 8 publications

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“…22,23 This software integrates a BLAST analysis against a nonredundant set of 289 sequences of interest and probe secondary structure analyses. 23 Two-hundred and thrity-six probes were obtained.…”

Section: Methodsmentioning

confidence: 99%

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Global analysis of DNA methylation and transcription of human repetitive sequences.

Horard¹,

Eymery²,

Fourel³

et al. 2009

Epigenetics

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Epigenetics 339Half of the human genome consists of repetitive DNA sequences. Recent studies in various organisms highlight the role of chromatin regulation of repetitive DNA in gene regulation as well as in maintainance of chromosomes and genome integrity. Hence, repetitive DNA sequences might be potential "sensors" for chromatin changes associated with pathogenesis. Therefore, we developed a new genomic tool called RepArray. RepArray is a repeat-specific microarray composed of a representative set of human repeated sequences including transposon-derived repeats, simple sequences repeats, tandemly repeated sequences such as centromeres and telomeres. We showed that combined to anti-methylcytosine immunoprecipitation assay, the RepArray can be used to generate repeat-specific methylation maps. Using cell lines impaired chemically or genetically for DNA methyltransferases activities, we were able to distinguish different epigenomes demonstrating that repeats can be used as markers of genome-wide methylation changes. Besides, using a well-documented system model, the thermal stress, we demonstrated that RepArray is also a fast and reliable tool to obtain an overview of overall transcriptional activity on whole repetitive compartment in a given cell type. Thus, the RepArray represents the first valuable tool for systematic and genome-wide analyses of the methylation and transcriptional status of the repetitive counterpart of the human genome.

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Section: Methodsmentioning

confidence: 99%

“…Table 3). The oligonucleotide probes were designed using OligoArray2.0 software 22,23 with defaults parameters. An antisense probe was then deduced from each sense probe.…”

Section: Introductionmentioning

confidence: 99%

Global analysis of DNA methylation and transcription of human repetitive sequences.

Horard¹,

Eymery²,

Fourel³

et al. 2009

Epigenetics

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“…Oligonucleotide probes were designed for a total of 383 S. aureus genes using the OligoArray program (Rouillard et al, 2002). Each oligonucleotide was a 50mer with a calculated T m of approximately 80 uC and minimal internal structure.…”

Section: Methodsmentioning

confidence: 99%

“…staphylococcal enterotoxin E) and positive control genes were included. The positive controls were the seven house-keeping genes used in Multi Locus Sequence Typing (MLST) (Enright & Spratt, 1999;Enright et al, 2000;van Leeuwen et al, 2003) together with the 16S and 23S rRNA subunits.Oligonucleotide probes were designed for a total of 383 S. aureus genes using the OligoArray program (Rouillard et al, 2002). Each oligonucleotide was a 50mer with a calculated T m of approximately 80 uC and minimal internal structure.…”

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confidence: 99%

A virulence-associated gene microarray: a tool for investigation of the evolution and pathogenic potential of Staphylococcus aureus

Saunders

Underwood

Kearns³

et al. 2004

Microbiology

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An oligonucleotide probe microarray for investigation of the evolution of epidemic Staphylococcus aureus strains has been constructed. The array comprises 383 probes based on virulence-associated genes present in four key strains. Twelve strains including seven for which the complete chromosomal nucleotide sequence was available were tested on the array. Twenty-six per cent of the probes were able to differentiate between strains to give a minimum of two gene differences between pairs. A gene difference distance tree based on the array data had approximately the same topology as one prepared using concatenated MLST sequences. Differences in the topologies of these trees were found to indicate that large-scale recombination events had occurred during the evolution of the species. One such occurrence appears to have been a key event in the genesis of the EMRSA-15 clone (ST22) that currently represents the most prevalent methicillin-resistant S. aureus (MRSA) in the UK. INTRODUCTIONStaphylococcus aureus is an important human pathogen responsible for bacterial infections seen both in the community and in hospitals. Over the last decades the emergence of multi-drug resistant strains has greatly increased the economic and health importance of staphylococcal infection (Chambers, 2001;Stefani & Varaldo, 2003;Wenzel, 1982). S. aureus is a highly adapted and extremely successful colonizer of the human nasopharynx, other mucosal surfaces and skin (Kluytmans et al., 1997;Williams, 1963). Colonization is generally asymptomatic but occasionally results in disease with a wide variety of signs and symptoms. These range from mild self-limiting infections of the skin to fulminating septicaemia (Lowy, 1998;Projan & Novick, 1997). Staphylococcal disease appears to result from an imbalance between the bacterium and the immune system and is associated with tissue invasion or unchecked growth. S. aureus is able to maintain its colonist status by producing a variety of proteins that interact with host-cell components (Baba et al., 2002;Kuroda et al., 2001). These proteins are described as virulence-associated and have functions such as extracellular matrix binding and host cell lysis. Expression of the S. aureus virulence-associated proteins is very carefully controlled by means of a network of regulatory genes including the agr and sar operons (Chien & Cheung, 1998;Sabersheikh & Saunders, 2004). Strain variation in these regulatory mechanisms may be an important factor influencing the switch from colonization to disease. Such variations may also contribute towards the success of the species by helping to minimize the emergence of immunity to essential S. aureus-specific antigens.Genome sequencing has shown that the species maintains a large number of virulence-associated genes but that not all are carried by each individual strain (Baba et al., 2002;Holden et al., 2004;Kuroda et al., 2001). Pairwise comparisons show as much as 20 % variation in the gene inventory of different S. aureus with most of the difference contributed by virule...

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“…Probesel [15], Promide [16], OligoArray [17], [18], and Thermonucleotide-BLAST [19] estimate probe specificity based on more accurate DNA thermodynamics. Some tiling-specific approaches focus on selecting probes in fixed windows [20], [21] but most practically relevant approaches rely on ad hoc methods and do not explicitly state more than one quality criterion for filtering the possible probes [22].…”

mentioning

confidence: 99%

Selecting Oligonucleotide Probes for Whole-Genome Tiling Arrays with a Cross-Hybridization Potential

Hafemeister

Krause

Schliep

2011

IEEE/ACM Trans. Comput. Biol. and Bioinf.

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Abstract-For designing oligonucleotide tiling arrays popular, current methods still rely on simple criteria like Hamming distance or longest common factors, neglecting base stacking effects which strongly contribute to binding energies. Consequently, probes are often prone to cross-hybridization which reduces the signal-to-noise ratio and complicates downstream analysis. We propose the first computationally efficient method using hybridization energy to identify specific oligonucleotide probes. Our Cross-Hybridization Potential (CHP) is computed with a Nearest Neighbor Alignment, which efficiently estimates a lower bound for the Gibbs free energy of the duplex formed by two DNA sequences of bounded length. It is derived from our simplified reformulation of t-gap insertion-deletionlike metrics. The computations are accelerated by a filter using weighted ungapped q-grams to arrive at seeds. The computation of the CHP is implemented in our software OSProbes, available under the GPL, which computes sets of viable probe candidates. The user can choose a trade-off between running time and quality of probes selected. We obtain very favorable results in comparison with prior approaches with respect to specificity and sensitivity for cross-hybridization and genome coverage with high-specificity probes. The combination of OSProbes and our Tileomatic method, which computes optimal tiling paths from candidate sets, yields globally optimal tiling arrays, balancing probe distance, hybridization conditions, and uniqueness of hybridization.

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OligoArray: genome-scale oligonucleotide design for microarrays

Abstract: The program code is distributed under the GNU General Public License and is freely available for non-profit use via request from the authors.

Cited by 148 publications

References 8 publications

Global analysis of DNA methylation and transcription of human repetitive sequences.

Global analysis of DNA methylation and transcription of human repetitive sequences.

A virulence-associated gene microarray: a tool for investigation of the evolution and pathogenic potential of Staphylococcus aureus

Selecting Oligonucleotide Probes for Whole-Genome Tiling Arrays with a Cross-Hybridization Potential

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