SHOW (Structured HOmogeneities Watcher) is a set of programs implementing different uses of Hidden Markov Models (HMMs) for DNA sequences. SHOW enables self-learning of HMM on a set of sequences, sequence segmentation based on the Baum-Welch or the Viterbi algorithms,and sequence simulation under a given HMM. We have designed these programs to allow the user to specify any highly structured model and also to process large sets of sequences. To date it has been successfully used in diverse tasks such as DNA segmentation in homogeneous segments, bacterial gene prediction and human splice sites detection.
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