Assessing the optimal number of HMM coding branches. Performance curves for 1,2,3 and 4 Markov branches of looped codon submodels for E. coli. The performance curves are made by the following procedure: First we sort the positive R-values in ascending order for each of the 10 subsets of set T (test sets). Then for each ascending R-value we calculate the fraction of genes in set T scoring below R (true positive rate) and the fraction of ORFs (with lengths greater than or equal to 20 codons) in one megabase double-stranded sequence scoring below R (false positive rate). The resulting 10 files with true and false positive rates are concatenated and 30 false positive cutoffs are selected (from 0 to 0.15 with steps of 0.005). The false positive entries in the 10 files which fall between these cutoffs are found and the corresponding true positive entries are averaged. Hence for each average false positive rate (halfway between two consecutive false positive cutoffs) we associate an average true positive rate and these tuples are then plotted.