MPRA Design Tool

This web-based graphical tool allows for rapid generation of .fa files suitable for MPRA experiments.

Massively parallel reporter assays (MPRAs) is an exciting platform which makes it possible to assay tens of thousands of short DNA sequences. The DNA is first synthesized on an array, and the oligos can subsequently be integrated into a plasmid which can be inserted into a cell. MPRAs have been used to study both promoters and enhancers to characterize the effect of regulatory sequences.

We have develop a user-friendly computational tool for designing the sequences that will be synthesized for the experiment:

• The first module allows the user to place different combinations of transcription factor binding motifs.
• The second module allows the user to explore different combinations of genetic variants from a VCF file.

In both cases we allow for a a modular design whereby spacers, restriction sites and barcodes can be arranged as desired.

Downloads

A web interface for a design involving transcription factor binding sites and genetic variants is available.