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

F Jaziri,J Denonfoux,P Peyret,E Peyretaillade,A Abid,J.-F Brugere,C Ribiere,A Mahul,D Boucher,C Gasc,N Parisot,D R C Hill

doi:10.1093/database/bau036

F Jaziri, J Denonfoux + Show 10 more

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https://doi.org/10.1093/database/bau036

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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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Prokaryotes are the most important and diverse group of organisms, widely distributed across almost all environmental habitats, even the most extreme, and involved in various ecological and environmental processes
To make all the phylogenetic oligonucleotide probes available, we developed a web interface (Figure 3) to fetch and download the 74 003 probes that compose our oligonucleotide database (PhylOPDb)
High-throughput molecular tools have opened an unprecedented opportunity for microbiology by enabling the culture-independent genetic study of complex microbial communities, which were so far largely unknown

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Prokaryotes are the most important and diverse group of organisms, widely distributed across almost all environmental habitats, even the most extreme, and involved in various ecological and environmental processes. Incorporating such data, molecular tools based on target-probe hybridization were developed to monitor microbial communities within complex environments. 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.

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