SPAR

SPAR processes and annotates small RNA sequencing (smRNA-seq) data to identify and characterize small non-coding RNA (sncRNA) genes and their processed products through reference-based and comparative analyses.

Key Features:

• Comprehensive Data Support: Supports small RNA-seq (smRNA-seq), short total RNA sequencing, microRNA-seq, and single-cell small RNA-seq protocols.
• Analysis and Visualization: Performs processing and generates comprehensive visualizations of small RNA-seq results.
• Extensive Annotation Capabilities: Integrates DASHR and ENCODE reference datasets covering 185 human tissues and cell types to annotate major small RNA types with genomic feature co-localization, precursor transcript cleavage patterns, and evolutionary conservation.
• Comparative Analysis: Enables comparison of experimental datasets against ENCODE and DASHR reference data to support discovery and characterization of sncRNA genes and specifically processed sncRNA products.
• Species Support: Supports human genomes hg19 and hg38 and mouse genome mm10.

Scientific Applications:

• sncRNA discovery and characterization: Facilitates systematic discovery and characterization of small non-coding RNA genes and processed sncRNA products from large-scale sequencing datasets.
• Gene regulation studies: Enables analysis of small RNA roles in gene regulation via annotation of genomic features and cleavage patterns.
• Disease mechanism and therapeutic target research: Supports investigation of disease mechanisms and identification of potential therapeutic targets involving small RNAs.

Methodology:

Integration of high-throughput small RNA sequencing data with DASHR and ENCODE reference databases for annotation and comparative analysis.