Some Results on Modeling Biological Sequences and Web Navigation with a Semi Markov Chain

Abstract

In the article, the entrance probabilities and the probability distribution of the number of transitions to a state are studied to provide some answers to questions related to state occupancies for the semi Markov model. Biological sequences and Web navigation are two cases that initially seem to be different but to a certain extent they do have similarities. Two main aspects of word occurrences in biological sequences are: (a) where do they occur and (b) how many times do they occur. In Web navigation the similar questions are (a) when a node is visited and (b) how many times a node is visited. So, the theoretical results of this study are applied to model these two cases and derive distributions of word location or node occurrence and frequency of occurrences. Rewards/costs are included in the Web navigation model and analytic forms for the means, variances, and moments of total interval rewards/costs are provided.