miRA

miRA identifies microRNA (miRNA) precursors in plant genomes by analyzing small RNA sequencing data together with a reference genome to predict precursor loci and evaluate precursor secondary structures and processing accuracy.

Key Features:

• Handling Complex Precursor Populations: Manages heterogeneous, non-conserved and species-specific precursor populations and diverse biogenesis pathways found in organisms such as Chlamydomonas reinhardtii.
• Evaluation of Secondary Structures and Processing Accuracy: Evaluates precursor secondary structures and processing accuracy as criteria for miRNA precursor identification.
• Flexibility and Adaptability: Provides flexible parameter settings tailored to species-specific characteristics and organisms lacking existing miRNA annotations.
• Output Formats: Generates output files in PDF, CSV, and genome-browser-compatible annotation formats for downstream genomic analyses.
• Novel miRNA Identification: Has identified novel miRNAs in Arabidopsis thaliana and Chlamydomonas reinhardtii and enabled discovery of miRNAs in related organisms such as Volvox carteri.
• Data Integration: Leverages small RNA sequencing data in conjunction with a reference genome to support precursor prediction.

Scientific Applications:

• Species-specific miRNA Characterization: Identification and annotation of non-conserved, species-specific miRNAs in plants with poorly characterized miRNA populations.
• Evolutionary Studies: Comparative analyses of miRNA landscapes across species such as Arabidopsis thaliana, Chlamydomonas reinhardtii, and Volvox carteri.
• Functional Genomics: Investigation of miRNA biogenesis pathways and regulatory mechanisms in diverse plant species.
• Discovery in Non-model Organisms: Discovery and annotation of novel miRNAs in organisms lacking cross-species conservation or existing annotations.

Methodology:

miRA requires small RNA sequencing data and a corresponding reference genome and assesses precursor secondary structures and processing accuracy to predict miRNA precursor loci.