in the -order model." The probability of base given the i previous bases is computed as follows. "The value of associated with can be regarded as a measure of confidence in the accuracy of this value as an estimate of the true probability. GLIMMER uses two criteria to determine . The first of these is simple frequency occurrence in which the number of occurrences of context string in the training data exceeds a specific threshold value, then is set to 1.0. The current default value for threshold is 400, which gives 95% confidence. When there are insufficient sample occurrences of a context string, build-imm employ additional criteria to determine value. For a given context string of length i, build-imm compare the observed frequencies of the following base , , , with the previously calculated interpolated Markov model probabilities using the next shorter context, , , , . Using a test, build-imm determine how likely it is that the four observed frequencies are consistent with the IMM values from the next shorter context." The second program called glimmer, then uses this IMM to identify putative gene in an entire genome. GLIMMER identifies all the open reading frame which score higher than threshold and check for overlapping genes. Resolving overlapping genes is explained in the next sub-section. Equations and explanation of the terms used above are taken from the paper 'Microbial gene identification using interpolated Markov models Resolving overlapping genes In GLIMMER 1.0, when two genes A and B overlap, the overlap region is scored. If A is longer than B, and if A scores higher on the overlap region, and if moving B's start site will not resolve the overlap, then B is rejected. GLIMMER 2.0 provided a better solution to resolve the overlap. In GLIMMER 2.0, when two potential genes A and B overlap, the overlap region is scored. Suppose gene A scores higher, four different orientations are considered. In the above case, moving of start sites does not remove the overlap. If A is significantly longer than B, then B is rejected or else both A and B are called genes, with a doubtful overlap. In the above case, moving of B can resolve the overlap, A and B can be called non overlapped genes but if B is significantly shorter than A, then B is rejected. In the above case, moving of A can resolve the overlap. A