A good intro can be found here: https://www.cs.huji.ac.il/course/2006/cbio/Scribes/lect14-assaf/lect14.pdf (in the context of motif finding, should be relevant). The main concept of MC is that there is a series of random variables which depend only on the value of the previous variable, it can be used to describe complex systems with a small set of parameters which are called transition probabilities (if the assumption that the value of a random variable depends only on the previous one holds).