MPRAnator

MPRAnator designs oligonucleotide sequences for massively parallel reporter assays (MPRAs) to enable systematic investigation of regulatory DNA elements, transcription factor (TF) occupancy, and the effects of single-nucleotide polymorphisms (SNPs) on gene regulation enabled by DNA synthesis and high-throughput sequencing.

Key Features:

• MPRA Motif Design: Provides precise control over motif placement within sequences using customizable variables to probe rules governing transcription factor (TF) occupancy.
• Single-Nucleotide Polymorphism (SNP) Design: Enables systematic examination of the functional effects of single or combinations of SNPs within regulatory sequences.
• Transmutation Tool: Generates negative controls by scrambling, reversing, complementing, or introducing multiple random mutations into input sequences or motifs.

Scientific Applications:

• Transcription factor binding analysis: Investigates contributions of transcription factor binding sites to regulatory activity through systematic motif placement and variation.
• Regulatory variant functional assessment: Assesses the impact of SNPs and variant combinations on regulatory sequence activity and gene expression.
• Regulatory sequence interaction studies: Explores interactions within regulatory regions that influence gene expression using large-scale designed sequence libraries for MPRA experiments.

Methodology:

Implemented using Python, Perl, and JavaScript.