IsomiR_Find

IsomiR_Find identifies phenotype-related single nucleotide polymorphisms (SNPs) and isoform microRNAs (isomiRs) by mapping 1000 Genomes Project SNPs onto pre-miRNA sequences and verifying isomiRs with individual miRNA sequencing data to support disease risk assessment and biomarker discovery.

Key Features:

• Integration of SNP Data: Maps SNPs from the 1000 Genomes Project to pre-miRNA sequences using whole-genome coordinates to locate variants that may influence miRNA splicing mechanisms.
• Construction of SNP-Pre-miRNA Sequences: Constructs SNP-pre-miRNA sequences to assess how genetic variants may impact miRNA maturation and functionality.
• Identification of Splicing Sites: Incorporates matpred2 to identify the four splicing sites of mature miRNAs for pinpointing isomiRs arising from alternative processing.
• Verification through Sequencing Data: Verifies the presence and relevance of identified isomiRs using individual miRNA sequencing data.

Scientific Applications:

• Disease Risk Assessment: Identifies phenotype-related SNPs and isomiRs to inform disease risk assessment, including cancer-related phenotypes.
• Biomarker Discovery: Supports discovery of novel miRNA-based biomarkers by linking SNP-induced isomiRs to specific phenotypes.
• Functional Mining of miRNAs and SNPs: Enables exploration of the functional implications of SNPs on miRNA processing and function via isomiR identification.

Methodology:

Maps SNPs from the 1000 Genomes Project to pre-miRNA sequences using whole-genome coordinates, constructs SNP-pre-miRNA sequences, applies matpred2 to identify the four splicing sites of mature miRNAs, and verifies isomiRs with individual miRNA sequencing data in an analysis of individual samples.