TruHmm

TruHmm assembles full-length transcripts in prokaryotes from directional RNA-seq short reads to characterize transcriptome structure and transcriptional variation.

Key Features:

• Directional RNA-Seq Integration: Operates on directional RNA-seq short reads to reconstruct transcript orientation and full-length sequences.
• Complex Transcriptome Profiling: Applied to E. coli K12, it identified that 46.9%–63.4% of operons are alternatively transcribed, 72.23%–89.54% of genes have antisense RNA (asRNA) transcripts, and 51.37%–72.74% of intergenic regions contain non-coding RNA (ncRNA) transcripts.
• Robust Algorithm: Employs a highly accurate assembly algorithm to reliably reconstruct full-length transcripts in complex prokaryotic transcriptomes.

Scientific Applications:

• Transcriptome Complexity Analysis: Characterizes alternative transcription, antisense RNA, and ncRNA distributions to analyze prokaryotic transcriptome complexity.
• Gene Expression Studies: Provides full-length transcript reconstructions for analyzing gene expression changes across environmental conditions and growth phases.
• Model Organism Research: Applied to E. coli K12 to reveal transcript variants and regulatory elements, providing a framework for studies in other prokaryotic models.

Methodology:

Reference-based assembly of full-length prokaryotic transcripts from directional RNA-seq short reads using an internal assembly algorithm.