Bcheck rnpB server

Bcheck rnpB server predicts RNase P RNA (rnpB) genes in genomic and metagenomic sequence data, combining rapid descriptor-based scanning and covariance-model validation to produce sensitive and subfamily-classified gene predictions.

Key Features:

• Hybrid Model Approach: Uses subfamily-specific descriptor models for rapid initial scanning and covariance models for sensitive, detailed RNase P RNA gene prediction.
• High Throughput Performance: Identified RNase P RNA genes in 98% of 1024 microbial chromosomal sequences within four hours on a single CPU.
• Comprehensive Database Coverage: Tested across metazoan and fungal eukaryotic chromosomes, accurately predicting known RNase P RNA genes and identifying novel ones, particularly in fungi.
• Gene Duplication Insights: Detects gene duplication events, observed in at least 20 metazoan organisms.
• Metagenomic Scale Application: Applied to the Global Ocean Sampling Expedition metagenomic dataset, predicting 2909 unique genes from over 10 million sequences (18 Gigabases).

Scientific Applications:

• Microbial Genomics: Scans microbial genomes to predict RNase P RNA genes, providing more intact structural predictions compared to existing annotations and classifying genes by subfamily membership.
• Eukaryotic Genomics: Identifies RNase P RNA genes across eukaryotic genomes with notable success in metazoan and fungal datasets and enables detection of gene duplications.
• Metagenomic Analysis: Enables large-scale metagenomic surveys, as demonstrated by the Global Ocean Sampling Expedition analysis that yielded 2909 unique RNase P RNA genes from over 10 million sequences (18 Gigabases).

Methodology:

Performs initial rapid descriptor-based filtering using subfamily-specific descriptor models to identify candidates, followed by construction and application of covariance models for sensitive, high-quality RNase P RNA gene model creation and validation.