MetaExploArrays: A Large-Scale Oligonucleotide Probe Design Software for Explorative DNA Microarrays

Jaziri, Faouzi; Hill, David R.C.; Parisot, Nicolas; Denonfoux, Jérémie; Dugat-Bony, Éric; Peyretaillade, Éric; Peyret, Pierre

doi:10.1109/pdcat.2012.94

Cited by 2 publications

(3 citation statements)

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“…In our future work, we will discuss the integration of our approach in a probe selection tool such as 'Metabolic Design' [6] or 'MetaExploArrays' [31] to allow the selection of probes from a group of nucleotide sequences or proteins according to the needs of the user. It can be easily integrated into probe selection tools.…”

Section: Future Workmentioning

confidence: 99%

“…It can be easily integrated into probe selection tools. In our future work, we will discuss the integration of our approach in a probe selection tool such as 'Metabolic Design' [6] or 'MetaExploArrays' [31] to allow the selection of probes from a group of nucleotide sequences or proteins according to the needs of the user. Selected probes will then be added to our oligonucleotide probe database [32], which is freely accessible via a web interface at http://g2im.u-clermont1.fr/phylopdb/.…”

Section: Future Workmentioning

confidence: 99%

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High performance computing of oligopeptides complete backtranslation applied to DNA microarray probe design

Jaziri

Peyretaillade

Peyret

et al. 2014

Concurrency and Computation

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Complete backtranslation is the step of generating all possible nucleic acid sequences from a protein sequence. This is a time-consuming task that can provide unreasonable quantities of data. Complete backtranslation was recently used to initiate probe design for functional DNA microarrays from conserved peptidic regions, in order to assess the full microbial gene diversity present in complex environments. In this article, we present an efficient parallelization method to compute a complete backtranslation of short peptides to select probes for functional microarrays. We implemented a software that uses meta-programming and a model-driven engineering approach to automatically generate source codes to perform complete backtranslation on different architectures: PCs, Symmetric Multiprocessors servers, computing clusters, or a computing grid. Our software is filtering the generated oligonucleotides with usual selection criteria for the design of microarray probes. It uses load balancing and can be easily integrated in probe design software for functional microarrays. We present its performance on both simulated and real biological datasets. The obtained results show a significant computing speedup on different platforms and an important gain of about 40% of disk space when filtering oligonucleotides.

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Section: Future Workmentioning

confidence: 99%

Section: Future Workmentioning

confidence: 99%

High performance computing of oligopeptides complete backtranslation applied to DNA microarray probe design

Jaziri

Peyretaillade

Peyret

et al. 2014

Concurrency and Computation

Self Cite

View full text Add to dashboard Cite

show abstract

“…However, it is also important to define explorative probes that can detect uncharacterized phylogenetic signatures and anticipate genetic variations ( 12 ). Currently, only four software programs allow the selection of explorative phylogenetic probes: PhylArray ( 13 ), PhylGrid ( 14 ), KASpOD ( 15 ) and MetaExploArrays ( 16 ).…”

Section: Introductionmentioning

confidence: 99%

PhylOPDb: a 16S rRNA oligonucleotide probe database for prokaryotic identification

et al. 2014

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In recent years, high-throughput molecular tools have led to an exponential growth of available 16S rRNA gene sequences. Incorporating such data, molecular tools based on target-probe hybridization were developed to monitor microbial communities within complex environments. Unfortunately, only a few 16S rRNA gene-targeted probe collections were described. Here, we present PhylOPDb, an online resource for a comprehensive phylogenetic oligonucleotide probe database. PhylOPDb provides a convivial and easy-to-use web interface to browse both regular and explorative 16S rRNA-targeted probes. Such probes set or subset could be used to globally monitor known and unknown prokaryotic communities through various techniques including DNA microarrays, polymerase chain reaction (PCR), fluorescent in situ hybridization (FISH), targeted gene capture or in silico rapid sequence identification. PhylOPDb contains 74 003 25-mer probes targeting 2178 genera including Bacteria and Archaea.Database URL: http://g2im.u-clermont1.fr/phylopdb/

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MetaExploArrays: A Large-Scale Oligonucleotide Probe Design Software for Explorative DNA Microarrays

Cited by 2 publications

References 20 publications

High performance computing of oligopeptides complete backtranslation applied to DNA microarray probe design

High performance computing of oligopeptides complete backtranslation applied to DNA microarray probe design

PhylOPDb: a 16S rRNA oligonucleotide probe database for prokaryotic identification

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