ImiRP

ImiRP performs selective mutagenesis of microRNA (miRNA) target sites in messenger RNA (mRNA) sequences to introduce specified mutations while preventing creation of new illegitimate miRNA target sites.

Key Features:

• Selective mutagenesis: Mutates specified predicted miRNA target sites in an input sequence while preventing formation of new illegitimate miRNA target sites.
• Parameter specification: Allows specification of species, mutation strategy, and types of disallowed illegitimate target sites.
• miRBase-based target comparison: Compares target site predictions between input and mutant sequences using the miRBase high-confidence miRNA dataset to identify potential illegitimate sites.
• Support for complex mutagenesis: Supports mutagenesis of single and multiple miRNA target sites, including overlapping sites relevant to microRNA cooperativity.
• Java-based modular implementation: Implemented as a modular Java system for sequence manipulation and mutation generation.

Scientific Applications:

• miRNA–mRNA interaction validation: Enables experimental validation of predicted miRNA target sites by producing mutant mRNA sequences that disrupt specific interactions.
• Functional impact assessment: Facilitates determination of the functional impact of individual miRNAs on their mRNA targets via targeted site disruption.
• Study of cooperativity and regulatory networks: Supports simultaneous disruption of multiple target sites to probe microRNA cooperativity and complex post-transcriptional regulatory networks.

Methodology:

Input specification of a sequence with predicted miRNA target sites; parameter setting of species, mutation strategy, and disallowed illegitimate site types; generation of candidate mutations with checks against the miRBase high-confidence miRNA dataset to detect illegitimate sites; assembly of a final mutant sequence containing the specified mutations and no new illegitimate sites.