RSSVM

RSSVM identifies functional cis-regulatory RNA motifs by combining RNA Sampler predictions of RNA secondary structure with Support Vector Machine classification to detect post-transcriptional regulatory elements in bacteria.

Key Features:

• Integration of RNA Sampler and SVM: Combines RNA Sampler predictions of common RNA secondary structures with Support Vector Machine classification for structural alignment and feature representation of RNA motifs.
• Distinctive Feature Set: Represents RNA secondary structures using a unique set of structural features that distinguish functional RNA motifs from random sequences.
• Training on Diverse Functional RNAs: Trains SVMs on functional RNAs from various bacterial RNA motif and gene families spanning a wide range of sequence identities.
• High Sensitivity with Low False Positive Rate: Demonstrates higher sensitivity than other RNA identification programs while maintaining an equivalent false positive rate when evaluated against known and random RNA motifs, enabling detection at low sequence identity.

Scientific Applications:

• Large-Scale Identification of Regulatory RNAs: Enables large-scale discovery of cis-regulatory RNA motifs to study post-transcriptional gene regulation in bacterial systems.
• Genome-Wide Discovery Pipeline: Supports genome-wide exploration of regulatory RNA motifs by combining RNA Sampler predictions with SVM classification.
• Application to Shewanella Genomes: Applied to Shewanella genomes (e.g., S. oneidensis) to identify putative regulatory RNA motifs in 5' untranslated regions of orthologous operons, including Rfam-annotated motifs and novel candidates supported by literature.
• Comprehensive Gene Regulation Insights: Contributes to identification of both DNA and RNA cis-regulatory elements to provide integrated insights into bacterial gene regulation.

Methodology:

Uses RNA Sampler to predict common RNA secondary structures, derives structural feature representations, and trains Support Vector Machines on these features to classify functional cis-regulatory RNA motifs.