Directed terminal restriction analysis tool (DRAT): an aid to enzyme selection for directed terminal‐restriction fragment length polymorphisms

Summary 1. T‐RFLP is an established tool for high‐throughput studies of microbial communities, which can, with care and practical validation, be enhanced to aid identification of specific organisms in a community by associating T‐RFs from experimental runs with predicted T‐RFs from a set of existing sequences. A barrier to this approach is the laborious process of selecting diagnostic restriction enzyme(s) for further validation. 2. Here, we describe directed terminal restriction analysis tool (DRAT), a software tool that aids the design of directed terminal‐restriction fragment length polymorphism (DT‐RFLP) strategies, to separate DNA targets based on restriction enzyme polymorphisms. The software assesses multiple user‐supplied DNA sequences, ranks optimal restriction endonucleases for separating targets and provides summary information including the length of diagnostic terminal restriction fragments. A worked example suggesting enzymes uniquely separating selected arbuscular mycorrhizal fungal groups is presented. 3. This tool greatly facilitates identification of diagnostic restriction enzymes for user‐designated groups within complex populations and provides expected product sizes for all designated groups.