MIPgen: optimized modeling and design of molecular inversion probes for targeted resequencing

Bioinformatics. 2014 Sep 15;30(18):2670-2. doi: 10.1093/bioinformatics/btu353. Epub 2014 May 26.


Molecular inversion probes (MIPs) enable cost-effective multiplex targeted gene resequencing in large cohorts. However, the design of individual MIPs is a critical parameter governing the performance of this technology with respect to capture uniformity and specificity. MIPgen is a user-friendly package that simplifies the process of designing custom MIP assays to arbitrary targets. New logistic and SVM-derived models enable in silico predictions of assay success, and assay redesign exhibits improved coverage uniformity relative to previous methods, which in turn improves the utility of MIPs for cost-effective targeted sequencing for candidate gene validation and for diagnostic sequencing in a clinical setting.

Availability and implementation: MIPgen is implemented in C++. Source code and accompanying Python scripts are available at http://shendurelab.github.io/MIPGEN/.

Publication types

  • Research Support, N.I.H., Extramural

MeSH terms

  • Algorithms*
  • Computational Biology / methods*
  • Computer Simulation
  • DNA Probes / genetics*
  • Humans
  • Models, Statistical*
  • Sequence Analysis / methods*


  • DNA Probes