segmentSeq

segmentSeq identifies small interfering RNA (siRNA) precursor loci by segmenting small RNA high-throughput sequencing data across multiple biological samples to infer double-stranded RNA precursors.

Key Features:

• Bioconductor package: Implemented as a Bioconductor package (version 1.5.6 and above).
• Simultaneous Segmentation: Performs concurrent segmentation of small RNA sequencing data across multiple samples to derive genomic segments.
• Replicate Data Integration: Integrates replicate information to produce a consensus segmentation that accounts for biological variability.
• Precursor Inference: Infers locations of double-stranded RNA precursors from siRNA mapping patterns.
• Application to Discovery: Applicable to small RNA high-throughput sequencing experiments for discovery of small RNA loci and novel mRNA transcripts.
• Demonstrated Datasets: Demonstrated on Arabidopsis thaliana and simulated datasets.

Scientific Applications:

• siRNA precursor characterization: Identification and characterization of siRNA precursors to study RNA interference and gene regulation.
• Small RNA locus discovery: Detection of small RNA-producing loci from high-throughput small RNA sequencing data.
• Comparative analysis: Consensus segmentation across samples and replicates for comparative analyses of siRNA expression and biogenesis.

Methodology:

Performs segmentation of high-throughput small RNA sequencing data across multiple biological samples, integrates replicate information, and constructs a consensus segmentation to infer locations of double-stranded RNA (siRNA) precursors.