Systems, Algorithms, and Software for Molecular Inversion Probe (MIP) Design

摘要

Methods and apparatus are provided for designing molecular inversion probes (MIPs). A computing device can determine representations of sequence features of a reference genome. The computing device can assess target arms that meet design criteria for a MIP in matching the representations of sequence features. For each pair of target arms that meet the design criteria, the computing device can: determine MIP performance data features for the pair, and determine a score for the pair using a MIP performance model operating on the MIP performance data features for the pair. The computing device can determine a subset of the target arms that collectively tile all of the sequence features, where the subset is determined based on the target arm scores. The computing device can determine designed MIPs based on the subset of target arms. The computing device can output information about each designed MIP.

主权项

1. A method, comprising:
determining, at a computing device, one or more representations of sequence features of a reference genome; assessing a set of possible target arms that meet one or more design criteria for a molecular interface probe (MIP) in matching the one or more representations of sequence features using the computing device; for each possible pair of target arms in the set of possible target arms that meet the one or more design criteria, the computing device:
determining MIP performance data features for the pair of possible target arms, anddetermining a score for the pair of possible target arms using a MIP performance model operating on the MIP performance data features for the pair of possible target arms; determining a subset of the set of possible target arms that tile each of the one or more representations of sequence features using the computing device, wherein the subset is determined based on the scores for the set of possible target arms; determining a set of designed MIPs based on the subset of the set of possible target arms that collectively tile all of the one or more representations of sequence features using the computing device; and providing an output comprising information about each designed MIP of the set of designed MIPs using the computing device.