sRNAtools

sRNAtools performs integrated discovery, profiling, and functional annotation of small noncoding RNAs from next-generation sequencing (NGS) small RNA data.

Key Features:

• Comprehensive sncRNA coverage: Supports microRNAs (miRNAs), isomiRs, Piwi-interacting RNAs (piRNAs), tRNA-derived fragments (tRFs), phased secondary small-interfering RNAs (phasiRNAs), plant-specific 24-nt short interfering RNAs (siRNAs), small nuclear RNAs (snRNAs), small nucleolar RNAs (snoRNAs), and ribosomal RNAs (rRNAs).
• Analysis modules: Provides single-case analysis, batch-case processing, group-case studies, and target-specific investigations as distinct analytical modules.
• Organism support: Accommodates analysis for up to 21 model organisms.
• Discovery and functional annotation: Performs identification of known and novel sncRNAs and supports downstream functional annotation.
• NGS data support: Operates on high-throughput/next-generation sequencing small RNA datasets.

Scientific Applications:

• Gene expression regulation: Profiling miRNAs and other sncRNAs involved in gene silencing and expression modulation.
• Cell proliferation studies: Investigating sncRNAs that influence cell growth and division processes.
• Novel RNA discovery: Identifying previously uncharacterized sncRNA species such as isomiRs, tRFs, phasiRNAs, and plant-specific 24-nt siRNAs.

Methodology:

Analyzes next-generation sequencing (NGS) small RNA data using analytical modules for single-case, batch-case, group-case, and target-specific analyses.