BrumiR

BrumiR identifies novel microRNAs (miRNAs) de novo from small RNA sequencing (sRNA-seq) data to enable characterization of miRNA expression, isomiRs, and other small RNAs.

Key Features:

• De Novo Discovery: Identifies miRNAs directly from sRNA-seq reads without reliance on a reference genome.
• Benchmarking and Performance: Demonstrates superior recall on real and simulated sRNA-seq datasets from animal and plant species.
• Efficiency and Speed: Maintains high computational efficiency and speed for analysis of numerous sRNA-seq datasets.
• Comprehensive Detection: Detects additional expressed sequences including small RNAs (sRNAs) and isomiRs.
• Reference Genome Integration (BrumiR2ref): Provides an auxiliary exhaustive post-hoc search to identify precursor sequences when a reference genome is available.

Scientific Applications:

• Non-model organism miRNA discovery: Enables identification of miRNAs in species lacking high-quality genomes or reference assemblies.
• Cross-kingdom studies: Applicable to sRNA-seq datasets from both animal and plant species.
• Large-scale sRNA-seq analyses: Supports high-throughput studies of miRNA expression, isomiR diversity, and other small RNAs.
• miRNA functional studies: Facilitates investigation of miRNA roles in gene regulation by providing novel miRNA and variant sequences.

Methodology:

BrumiR constructs and analyzes de Bruijn graphs from sRNA-seq reads to identify novel miRNAs through direct examination of sequencing reads; when a reference genome is available, BrumiR2ref performs an exhaustive post-hoc search to identify precursor sequences.