PhylOPDb: a 16S rRNA oligonucleotide probe database for prokaryotic identification.
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/
Clermont Université, Université d'Auvergne, EA 4678 CIDAM, BP 10448, F-63001 Clermont-Ferrand, France, UMR CNRS 6158, ISIMA/LIMOS, Clermont Université, Université Blaise Pascal, F-63173 Aubière, France, CNRS, UMR 6023, LMGE, F-63171 Aubière, France and Clermont Université, CRRI, F-63177 Aubière, France.
Faouzi
F
Jaziri
Nicolas
N
Parisot
Anis
A
Abid
Jérémie
J
Denonfoux
Céline
C
Ribière
Cyrielle
C
Gasc
Delphine
D
Boucher
Jean-François
JF
Brugère
Antoine
A
Mahul
David R C
DR
Hill
Eric
E
Peyretaillade
Pierre
P
Peyret
D001419:Bacteria / Q000145:classification* / Q000235:genetics*; D003198:Computer Simulation; D030541:Databases, Genetic; D015345:Oligonucleotide Probes / Q000235:genetics*; D012336:RNA, Ribosomal, 16S / Q000235:genetics*; D014584:User-Computer Interface
D015345:Oligonucleotide Probes; D012336:RNA, Ribosomal, 16S