P-Finder

P-Finder identifies RNase P RNA genes (rnpB) in prokaryotic genomes, enabling sensitive and accurate annotation despite high sequence variability and structural diversity.

Key Features:

• Comprehensive RNase P RNA database: Leverages the largest known RNase P RNA database as a reference for detection.
• Local alignment scoring algorithm: Employs an advanced local alignment scoring algorithm for rnpB gene detection.
• High sensitivity and accuracy: Detects rnpB genes in nearly 99% of examined microbial genomes.
• Structural variability handling: Identifies diverse RNase P RNA structural classes, including C-type and minimal T-type RNAs, across at least five distinct prokaryotic structure types.
• Improved performance over covariance models: Addresses limitations of previous covariance model approaches that struggled with RNase P RNA structural variability.

Scientific Applications:

• Discovery of novel rnpB genes: Computationally identified four new rnpB genes encoding minimal T-type P RNase P RNAs.
• Identification of rare structural types: Detected the second C-type RNase P RNA in Sphaerobacter thermophilus.
• Evolutionary and symbiosis studies: Revealed absence of RNase P RNAs in several obligate endosymbionts of sap-sucking insects, suggesting a novel evolutionary adaptation.

Methodology:

Couples the largest known RNase P RNA database with a local alignment scoring algorithm to enhance sensitivity and speed relative to covariance model approaches.