miARma-Seq

miARma-Seq performs comprehensive analysis of miRNA, mRNA, and circular RNAs (circRNAs) from RNA sequencing (RNAseq) data to enable differential expression, miRNA–mRNA interaction prediction, and functional interpretation across sequenced organisms.

Key Features:

• Integrated multi-RNA analysis: Enables simultaneous identification and analysis of miRNA, mRNA, and circRNAs from RNAseq data.
• Differential expression analysis: Performs differential expression analysis to detect significant RNA level changes between conditions or sample groups.
• miRNA–mRNA target prediction and functional analysis: Predicts interactions between miRNAs and mRNA targets and supports downstream functional analysis.
• Scalability (multithread architecture): Implements a multithread architecture to process large RNAseq datasets efficiently.
• Integration of established bioinformatics tools: Integrates several established bioinformatics tools into a cohesive framework to enable robust analyses.
• Cross-species support: Applicable to RNAseq data from various sequenced organisms.

Scientific Applications:

• Transcriptomic profiling: Comprehensive profiling of miRNA, mRNA, and circRNA expression from RNAseq experiments.
• Differential expression studies: Identification of RNAs with significant expression changes between experimental conditions or sample groups.
• RNA interaction and regulatory network analysis: Analysis of miRNA–mRNA interactions to investigate gene regulatory networks.
• Non-coding RNA functional studies and disease mechanism research: Functional analysis to infer biological roles of miRNAs and circRNAs, including studies of disease-associated non-coding RNA mechanisms.

Methodology:

The pipeline integrates several established bioinformatics tools into a cohesive framework and has been tested on validated datasets.