Files in this Data Supplement:
Supplemental Materials and Methods (formamide dissociation profiles for model development, curve fitting and statistics, updated mechanistic model of FISH, single-reaction model with a FISH-specific free-energy definition for improved predictions, using the single-reaction model as a predictor of mismatch stability, dual-probe use to increase specificity and confidence level in target identification, detailed description of probe design algorithm, demonstration of dual-probe design, analysis of 16S rRNA probes in probeBase); probes used in modeling (Table S1); model development, comparison, and statistics (Table S2); nearest-neighbor parameters (Table S3); moderate- and low-coverage 16S probes published in literature (Table S4); moderate- and low-specificity 16S probes published in literature (Table S5); phylum-specific probes in probeBase that were similar to those designed with DECIPHER (Table S6); experimental and theoretical formamide dissociation profiles (Fig. S1); formamide dissociation profiles and melting point predictions with selected models (Fig. S2); relationship between original nearest-neighbor free energies and best-fitting parameters used in nearest-neighbor model (Fig. S3); correlation of experimental and theoretical Δ[FA]m values for SRM and RMM (Fig. S4); derivation of a probability density function to describe predictive error on [FA]m based on leave-one-organism-out cross validation (LOOOCV) tests (Fig. S5); probe design algorithm (Fig. S6); screen shot of the 16S oligo page for targeting the genus Xenorhabdus using two probes (Fig. S7); screen shot of the 16S oligo page for targeting the genus Xenorhabdus using one probe (Fig. S8); selected phylogenetic trees showing probability of hybridization with each probe in probeBase (Fig. S9).
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