In this Master's project, we will specifically address the following aspects of the problem:
- A simple alignment method to find matches between a target sequence and closely related groups of sequence fragments. This is a rather simple part of the problem. The only challenge to overcome is the multiple matches of some sequence fragments to the target sequence.
- An advanced alignment method to detect matches between a target sequence and distantly related groups of sequence fragments. To address this part of the problem, we would need to use techniques such as sequence profiling and possibly secondary structure prediction.
We expect that by the end of this project we will have a framework to potentially extract (both closely and distantly) related groups of sequence fragments for a given target sequence.