MIPgen

MIPgen designs Molecular Inversion Probes (MIPs) for targeted gene resequencing, optimizing capture uniformity and specificity in multiplexed genomic assays.

Key Features:

• MIP design for multiplexing: Generates MIP designs targeting specific genomic loci for multiplexed targeted resequencing applications.
• Advanced predictive models: Employs logistic regression and Support Vector Machine (SVM)-derived models for in silico prediction of assay success.
• Redesign algorithms: Applies redesign algorithms to enhance coverage uniformity and probe performance compared to prior methods.
• Implementation: Implemented in C++ with accompanying Python scripts for computational processing and integration.

Scientific Applications:

• Targeted gene resequencing: Design of MIP assays for targeted resequencing of candidate genes and genomic loci.
• Diagnostic sequencing: Support for diagnostic sequencing workflows requiring specific and uniform capture of target regions.
• High-throughput multiplex studies: Enables simultaneous targeting of hundreds to thousands of loci for large-cohort or population-scale studies.

Methodology:

Uses logistic regression and SVM models for in silico assay success prediction and applies redesign algorithms to improve coverage uniformity; software implemented in C++ with Python scripts.