Large Scale Parallelization Method of 16S rRNA Probe Design Algorithm on Distributed Architecture: Application to Grid Computing

Missaoui, Mohieddine; Jaziri, Faouzi; Cipière, Sébastien; Hill, David R.C.; Peyret, Pierre

doi:10.1109/ici.2011.16

Cited by 2 publications

(2 citation statements)

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“…PhylGrid ( 14 ) is a large-scale probe design software linked to the EGI grid. It is an improvement of the PhylArray algorithm presented in Militon et al ( 13 ) that allows defining regular and explorative oligonucleotide probes targeting SSU rRNA genes at any phylogenetic level ( Figure 1 ).…”

Section: Database Construction and Developmentmentioning

confidence: 99%

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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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Section: Database Construction and Developmentmentioning

confidence: 99%

“…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%