AsiDesigner

AsiDesigner designs siRNAs targeting specific mRNA isoforms and conserved regions across alternative splice variants to enable isoform-specific and multi-isoform RNA interference (RNAi) experiments.

Key Features:

• Alternative Splicing Consideration: Identifies common target regions across multiple mRNA isoforms using a novel algorithm to enable isoform-specific or shared-isoform targeting.
• Multi-mRNA Silencing: Designs common siRNAs capable of silencing multiple mRNAs derived from alternatively spliced transcripts.
• Performance Scoring: Provides a scoring scheme that integrates key siRNA design factors to evaluate predicted efficacy.
• Off-Target Analysis: Performs stepwise off-target searches using BLAST and FASTA to identify potential unintended matches.
• Secondary Structure Evaluation: Calculates siRNA secondary structure energy to assess stability and folding properties.

Scientific Applications:

• Functional Genomics: Enables isoform-specific loss-of-function studies to dissect gene and protein function.
• Drug Discovery: Supports identification of isoform-specific therapeutic targets and development of RNAi-based interventions.
• Molecular Biology Research: Facilitates analysis of complex splicing patterns and genetic interactions by enabling targeted knockdown of specific isoforms.

Methodology:

Implements a novel algorithm to identify common target regions across multiple mRNA isoforms; conducts stepwise off-target searches using BLAST and FASTA; applies a scoring scheme integrating siRNA design factors; evaluates siRNA secondary structure energy.