PhylOPDb

PhylOPDb provides a curated database of 74,003 25-mer 16S rRNA-targeted oligonucleotide probes for phylogenetic identification and monitoring of prokaryotic (Bacteria and Archaea) communities.

Key Features:

• Extensive Probe Collection: Contains 74,003 curated 25-mer oligonucleotide probes targeting 2,178 genera across Bacteria and Archaea.
• Technique Support: Enables application of DNA microarrays, polymerase chain reaction (PCR), fluorescent in situ hybridization (FISH), targeted gene capture, and in silico rapid sequence identification.
• High-throughput Sequence Integration: Incorporates large-scale 16S rRNA gene sequence data to support probe coverage and selection.
• Target-Probe Hybridization Focus: Emphasizes probe-target hybridization strategies for detection and monitoring of prokaryotic taxa.

Scientific Applications:

• Global Community Monitoring: Facilitates monitoring of known and unknown prokaryotic communities across diverse environments.
• Microbial Diversity and Dynamics: Supports analysis of microbial diversity, community dynamics, ecology, and evolutionary relationships.
• Rapid In Silico Identification: Supports fast sequence-based identification of 16S rRNA sequences using probe matching and in silico methods.

Methodology:

Integrates high-throughput 16S rRNA gene sequence data and employs target-probe hybridization approaches alongside in silico rapid sequence identification.