Capturing diverse microbial sequence with comprehensive and scalable probe design

Hayden C. Metsky; Katherine J. Siddle; Adrianne Gladden-Young; James Qu; David K. Yang; Patrick Brehio; Andrew Goldfarb; Anne Piantadosi; Shirlee Wohl; Amber Carter; Aaron E. Lin; Kayla G. Barnes; Damien C. Tully; Björn Corleis; Scott Hennigan; Giselle Barbosa-Lima; Yasmine R. Vieira; Lauren M. Paul; Amanda L. Tan; Kimberly F. Garcia; Leda A. Parham; Ikponmwonsa Odia; Philomena Eromon; Onikepe A. Folarin; Augustine Goba; Etienne Simon-Lorière; Lisa Hensley; Angel Balmaseda; Eva Harris; Douglas Kwon; Todd M. Allen; Jonathan A. Runstadler; Sandra Smole; Fernando A. Bozza; Thiago M. L. Souza; Sharon Isern; Scott F. Michael; Ivette Lorenzana; Lee Gehrke; Irene Bosch; Gregory Ebel; Donald Grant; Christian Happi; Daniel J. Park; Andreas Gnirke; Pardis C. Sabeti; Christian B. Matranga

This framework for designing probes offers considerable flexibility. For example, it reduces the design to a problem of determining probe-target hybridization. The function f map , which determines whether a probe hybridizes to a range in a target sequence (and, if it does, precisely the range), can be customized by a user in CATCH's source code or can be provided in a command-line argument to be dynamically loaded. For example, although by default CATCH does not use a thermodynamic model of hybridization, a user could choose to incorporate a calculation of free energy to evaluate the likelihood of hybridization. Here, when computing s(d, θ d ), CATCH's default f map is based on three parameters in θ d : a number m of mismatches to tolerate, a length lcf of a longest common substring, and a length i of an island of an exact match. f map computes the longest common substring with at most m mismatches between the probe sequence and target subsequence, and returns that the probe covers the target range if and only if the length of this is at least lcf. Optionally (if i > 0), f map additionally requires that the probe and target subsequence share an exact (0-mismatch) match of length at least i to return that the probe covers the range. (See Supplementary Fig. 1b for a visual representation and "Exploring the parameter space across taxa" for example values.)