DEQOR

DEQOR predicts and scores siRNA candidates and evaluates their specificity for RNA interference (RNAi) experiments.

Key Features:

• Scoring System for siRNA Design: A scoring system evaluates inhibitory potency of siRNA sequences using parameters including sequence length, GC-content, and nucleotide composition.
• Identification of High Silencing Capacity Regions: Predicts regions within a gene with high silencing capacity by analyzing base pair composition.
• Cross-Silencing Evaluation: Performs BLAST searches against the transcriptome or genome to assess potential cross-silencing and off-target interactions.
• Support for Chemical Synthesis and Enzymatic Preparation: Supports design and evaluation of chemically synthesized siRNAs and endoribonuclease-prepared siRNAs (esiRNAs or "diced" RNAs).

Scientific Applications:

• Functional Genomics: Selection of specific siRNAs to investigate gene function via targeted mRNA degradation in RNAi experiments.
• Disease Mechanism Studies: Design of siRNAs to modulate gene expression for studying molecular mechanisms of disease.
• Therapeutic Development: Identification of siRNA candidates for development of RNAi-based therapeutic interventions.

Methodology:

Computational analysis of target mRNA sequences to identify optimal siRNA candidates; scoring based on sequence length, GC-content, and nucleotide composition; base pair composition analysis to locate high-silencing regions; and BLAST searches against transcriptome or genome sequences to evaluate specificity and potential cross-silencing.