hyb

hyb detects and annotates chimeric RNA molecules from high-throughput cDNA sequencing generated by Cross-linking, Ligation and Sequencing of Hybrids (CLASH) experiments to identify RNA-RNA interactions associated with protein complexes.

Key Features:

• CLASH data processing: Processes high-throughput cDNA sequencing data derived from Cross-linking, Ligation and Sequencing of Hybrids (CLASH) experiments.
• Chimera detection: Detects and annotates rare chimeric reads that physically join two interacting RNA molecules into a single sequence amid millions of non-chimeric reads.
• Argonaute (AGO) compatibility: Applicable to datasets derived from Argonaute (AGO) complexes and other experiments producing chimeric reads.
• Preprocessing: Performs read preprocessing using Flexbar.
• Read mapping: Employs Bowtie2 for read mapping to support alignment-based chimera detection.
• Comparative performance: Reported to achieve higher sensitivity, specificity, and computational efficiency in chimera detection compared with BLAST, BLAST+, BLAT, and pBLAT.

Scientific Applications:

• RNA-RNA interaction discovery: Identification of RNA-RNA interactions associated with protein complexes captured by CLASH.
• Post-transcriptional regulation studies: Analysis of interactions mediated by Argonaute (AGO) complexes to investigate post-transcriptional gene regulation.
• Regulatory network annotation: Annotation of chimeric reads to reveal interaction pairs that contribute to regulatory networks governing gene expression.

Methodology:

Preprocessing of sequencing reads using Flexbar followed by read mapping with Bowtie2, with reported improvements in sensitivity, specificity, and computational efficiency relative to BLAST, BLAST+, BLAT, and pBLAT.