There are a lot of data sequences, I am trying to find pairs of sequences that are similar with other.
Trivially, we can define some distance measure, and compare each pair of sequence in terms of this measure. Or even we can solve this problem in a clustering framework. I have two questions, what are the general features to capture the sequence type of data? If I want to solve the problem in the context of either classification or clustering, I have to find the way to characterize the sequence.
A side problem is that, two sequences may be different, but the subsequence of one may be similar to a sub sequence of another one. How to solve this problem in a systematic way? Are there some algorithms/models to handle this kind of problem? Using sliding window approach can make computation exponentially large.