How do I perform recurring pattern mining or regular expressions of nucleotide sequences?
I'm no expert in MATLAB but I know that it is possible to do regular expressions in MATLAB with the general rules explained here. However there are alternative approaches and softwares you could use to achieve this with softwares that are freely available and quite powerful in performing such functions. Although I'm aware that perl and python are the programs of choice for regular expression analysis; however I would urge you to consider the R language. R allows you to construct your mining results in a format of a table, which each column containing the data you are interested! there are many packages in R that allows you to process many data types. I would say R is worth the investment to learn for any future data analysis. I use the RStudio to interact with the R language software.

The best place to get help for MATLAB or R is the http://stackoverflow.com which you can sign on with you current account. In fact I have asked a few questions there on regular expressions and the community is very helpful however ensure that you show your attempt at the problem and where you are stuck in order to get a constructive responses!