This file explains challenges in computational biology, markov chains and hidden markov models, HMM (hidden markov model), typical HMM problems, CpG islands, training markov chains for CpG islands, decoding, the viterbi algorithm, generating a sequence by the model, the forward algorithm, relation between forward and viterbi, pseudocounts, the baum-welch algorithm, HMM architectural/topology design and VEIL: viterbi exon-intron locator.