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The aim of this study was to develop and evaluate SSRs in crape myrtles as well as to evaluate genetic diversity and to perform fingerprinting analysis.
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We also performed fingerprinting by short tandem repeat analysis (STR) and confirmed that all of the MiPSC5 and targeted sub-clones were derived from the same patient (Fig. S3D).
Using Coomassie stained gels we have isolated spots of expected pI for the Hsp70 family members and performed fingerprinting and microsequencing analysis as described previously [ 8].
The validity of clustering as a proxy for recent transmission might be challenged by the fact that we did not perform fingerprint analysis on all isolates (39).
At the same time, the microbiologist must also be able to rapidly confirm or exclude the possibility of an epidemic cluster by performing fingerprinting of the isolates [ 4- 6, 9].
Extended-connectivity fingerprints of diameter 4 and 6 are among the best performing fingerprints when ranking diverse structures by similarity, as is the topological torsion fingerprint.
Here we provide conclusive evidence that extended-connectivity fingerprints of diameter 4 and 6 are among the best performing fingerprints whether separating actives from decoys in a virtual screen or ranking diverse structures by similarity.
For example, while HashAP is the best performing fingerprint in the single-assay benchmark, its distance to TT (six positions below it in the graph) is 149 which corresponds to just 3.3%% of the dataset.
The single-assay benchmark presents a more challenging set of series to be ordered; one of the best performing fingerprints (HashAP) only gets the answer close to correct for 1744 of the 4563 cases (38%%).
If we consider the multi-assay benchmark first (Fig. 7), one of the best performing fingerprints (LECFP4) can reproduce or almost reproduce (off-by-one) the original series order in 2201 of the 3629 cases (61%%).
The AUC values achieved with the best performing fingerprint for each target are presented in Fig. 2 (cross-validation with error bars) and Fig. 3 (external validation) and those for all other fingerprints are available in the Supplementary Information (Additional file 1: Tables S3, S4).
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