MirTools

MirTools analyzes high-throughput small RNA sequencing data to profile, classify, annotate and quantify microRNAs (miRNAs), predict novel miRNAs, and identify differential expression in small RNA transcriptomes.

Key Features:

• Quality Control: Filters low-quality reads and removes 3'/5' adapters from raw sequencing data.
• Alignment and Exploration: Aligns large-scale short reads to a reference genome and reports length distribution of reads.
• Classification: Classifies small RNA candidates into known miRNAs, non-coding RNAs, genomic repeats, and coding sequences.
• Annotation and Quantification: Provides annotation for known miRNAs including counts of miRNA/miRNA* pairs in absolute and relative terms and identifies the most abundant tag per miRNA.
• Novel miRNA Prediction: Predicts novel miRNAs not present in existing annotations.
• Differential Expression Analysis: Identifies differentially expressed miRNAs between samples using two counting strategies: total read tag counts and most-abundant tag counts.

Scientific Applications:

• miRNA profiling: Generate abundance and length-distribution profiles of known miRNAs from deep-sequencing short reads.
• Novel miRNA discovery: Discover previously uncharacterized miRNAs from small RNA sequencing datasets.
• Small RNA transcriptome characterization: Characterize the composition of small RNA populations by classifying reads into miRNAs, non-coding RNAs, repeats, and coding-derived fragments.
• Comparative differential expression: Compare miRNA expression between samples using total read tag counts and most-abundant tag counts to detect differential expression.
• Studies of gene regulation: Support investigation of miRNA roles in biological processes such as development and tumorigenesis.

Methodology:

Computational steps explicitly include filtering low-quality reads, 3'/5' adapter removal, alignment of short reads to a reference genome, analysis of read length distribution, classification into known miRNAs/non-coding RNAs/genomic repeats/coding sequences, annotation and quantification of miRNA/miRNA* pairs and most-abundant tags, novel miRNA prediction, and differential expression analysis using total read tag counts and most-abundant tag counts.