IsomiR

IsomiR identifies and characterizes isomiRs from small RNA sequencing (small-RNA-seq) data, detecting length and sequence variants such as 5' and 3' end variations, untemplated additions, internal edits, and single nucleotide polymorphisms (SNPs).

Key Features:

• Systematic identification and quantification: Detects diverse isomiR types including 3' and 5' end variants, tailings, SNPs, RNA edits, and fuzzy combinations.
• Detection algorithm: Implements a novel algorithm capable of detecting diverse isomiR types with high confidence.
• Third-party tool integration: Integrates over ten third-party software tools to support comprehensive small-RNA-seq analyses.
• Database integration: Incorporates required databases for annotation and thorough analysis of isomiRs.
• Cross-kingdom analysis: Supports identification of non-coding RNAs and isomiRs in datasets from both animal and plant sources.
• Automated multi-dataset processing: Processes multiple datasets automatically without input file size restrictions.
• Validation on simulated data: Performance validated on simulated small-RNA-seq data with reported 100% accuracy in identifying correctly mapped reads and various isomiRs.

Scientific Applications:

• Basal Cell Carcinoma small-RNA-seq analysis: Applied to BCC datasets to reveal that miR-183-5p up-regulation in Nodular BCCs was primarily due to a novel 5' end variant.
• Functional impact and target identification: Enabled identification of a variant with a unique seed-region motif and targeting of mRNA isoforms associated with disease pathways.

Methodology:

Employs a novel algorithm to detect diverse isomiR types; integrates over ten third-party software tools and required databases; processes multiple datasets automatically without input file size restrictions; validated using simulated small-RNA-seq data demonstrating 100% accuracy in identifying correctly mapped reads and various isomiRs.