RNA-eXpress

RNA-eXpress identifies and annotates transcriptional features from next-generation sequencing (NGS) read alignments to enable comprehensive, annotation-independent transcriptome analysis.

Key Features:

• Annotation independence: Operates without relying on existing gene annotations to avoid bias toward known transcripts.
• Broad feature identification: Detects splice variants, large and small non-coding RNAs, novel transcription start sites, alternative promoters, RNA editing events, and processing of coding transcripts.
• Input and output formats: Accepts aligned reads in BAM format and produces study-specific feature annotations in GTF format, along with comparison statistics, sequence extraction, and feature counts.
• Computational efficiency: Optimized for rapid processing to support large-scale transcriptome analyses.
• Extensibility: Allows integration of new feature-identification algorithms via class extension.

Scientific Applications:

• Discovery of regulatory elements: Identification of novel promoters and transcription start sites to study gene regulation.
• Alternative splicing analysis: Characterization of splice variants and splicing mechanisms.
• Non-coding RNA studies: Detection and annotation of large and small non-coding RNAs to investigate their functions.
• RNA editing and processing research: Detection of RNA editing events and processing of coding transcripts to explore post-transcriptional modifications.

Methodology:

Processes NGS read alignments in BAM format without requiring pre-existing annotations to identify transcriptional and genomic features and outputs annotations in GTF plus comparison statistics, sequence extraction, and feature counts.