TRANSIT - A Software Tool for Himar1 TnSeq Analysis
Fig 2
The HMM is fully connected, allowing transitions between each of the states. Transition probabilities and parameters are estimated in such a way that the HMM will remain in the state which best represents the read-counts observed. (a) Essential regions (“ES”) are mostly devoid of insertions, (c) while non-essential regions (“NE”) contain read-counts around the global mean. (b) Growth-defect regions (“GD”), and (d) growth-advantage regions (“GA”) represent those areas with significantly suppressed or inflated read-counts.