Fig. 3

Six HMMs MAKER structural annotation method. The center workflow depicts the standard method for training hidden markov models for use in MAKER, while the low GC (top) and high GC (bottom) training methods can be used after creating high and low GC HMM training data sets. After separately training HMMs with the low and high GC training data, all three SNAP HMMs and all three AUGUSTUS HMMs were specified in the maker_opts.ctl file (see the Methods section), and MAKER was run to create the six HMMs annotation, which incorporates gene predictions from the standard, high and low GC MAKER runs