RNAmmer

RNAmmer predicts ribosomal RNA (rRNA) genes in complete genome sequences to enable accurate identification and annotation of 5S/8S, 16S/18S, and 23S/28S rRNAs across all kingdoms of life.

Key Features:

• Hidden Markov Models (HMMs): Employs HMMs trained on the 5S ribosomal RNA database and the European ribosomal RNA database project for rRNA gene prediction.
• Pre-screening step: Integrates a pre-screening step that increases analysis speed while maintaining sensitivity, enabling analysis of complete bacterial genomes in under a minute.
• High accuracy and novel detection: Demonstrates high accuracy in locating rRNA genes and can identify previously unannotated rRNA loci.
• Genome-scale scope: Operates on full genome sequences across all kingdoms of life and targets major rRNA species (5S/8S, 16S/18S, 23S/28S).

Scientific Applications:

• Comparative Genomics: Provides consistent rRNA annotations to support cross-species comparative analyses.
• Genomic Annotation: Enhances annotation of newly sequenced genomes by accurately identifying rRNA genes.
• Evolutionary Studies: Facilitates evolutionary and phylogenetic analyses by supplying validated rRNA sequences from diverse organisms.

Methodology:

Uses hidden Markov models trained on the 5S ribosomal RNA database and the European ribosomal RNA database project and applies a pre-screening step to speed genome-scale prediction of 5S/8S, 16S/18S, and 23S/28S rRNAs.