Figure 6

Comparison between sum-of-pair gap costs and linear gap costs in the retrieval of Ensemble annotated SNORA42 homologs in mouse. The figure shows the true positive rate (TPR) for identifying Ensembl-annotated Human SNORA42 homologs with respect to the total number of reported chains for both linear and sum-of-pair gap cost models. In case of the linear gap cost model, a wide range of values are selected for the weighting parameters and , i.e., . In the sum-of-pair gap cost model, the parameters and are chosen. Note that the number of reported chains for a given parameter set is entirely determined by the minimal required chain score. The average TPR of clasp using the linear gap cost model (, , dashed red line) is significantly lower compared to sum-of-pair gap cost model (solid black line). However, the performance of chaining with linear gap cost models heavily depends on the selection of parameters (shaded area).