We present a software tool, called cMatch, to reconstruct and identify synthetic genetic constructs from their sequences, or a set of sub-sequences - based on two practical pieces of information: their modular structure, and libraries of components. Although developed for combinatorial pathway
engineering problems and addressing their quality control (QC) bottleneck, cMatch is not restricted to these applications. QC takes place post assembly, transformation and growth. It has a simple goal, to verify that the genetic material contained in a cell matches what was intended to be built - and
when it is not the case, to locate the discrepancies and estimate their severity. In terms ofreproducibility/reliability, the QC step is crucial. Failure at this step requires repetition of the construction and/or sequencing steps.
When performed manually or semi-manually QC is an extremely time-consuming, error prone process, which scales very poorly with the number of constructs and their complexity. To make QC frictionless and more reliable, cMatch performs an operation we have called ‘construct-matching’ and automates it. Construct-matching is more thorough than simple sequence-matching, as it matches at the functional level-and quantifies the matching at the individual component level and across thewhole construct.