The correct term is **compare**:

- to examine (two or more objects, ideas, people, etc.) in order to note similarities and differences  ([Dictionary.com][1])
- to examine the character or qualities of especially in order to discover resemblances or differences  ([Merriam-Webster][2])

Because you are working with data and performing a detailed analysis of one or more aspects of these data sets, you could also use the term **analyze**.

- to study or determine the nature and relationship of the parts of by analysis ([Merriam-Webster][3])

However, this word lacks the specific meaning that you are looking at *two* things, not just one.

If you don't need a *single* word, you could state:

> I am going to *comprehensively identify the list of differences in context and structure*...

That is precise, but at the cost of being quite verbose.

  [1]: http://dictionary.reference.com/browse/compare
  [2]: http://www.merriam-webster.com/dictionary/compare
  [3]: http://www.merriam-webster.com/dictionary/analyze