In this master project, we would specifically be working on the following aspects of the problem:
- a simple alignment method to find matches between a target sequence and closely related sets ofsequence fragments. This is rather easier part of the problem. The only challenge one would have to deal with would be the multiple alignments of some sequence fragments to the target sequence.
- an advance alignment method to detect matches between a target sequence and remotely related sets of sequence fragments. To deal with this part of the problem, one would need to apply techniques such as sequence profiles, and possibly secondary structure prediction.
At the end of this project, we expect to have a framework where, for a given target sequence, one could extract potentially (both closely and remotely) related sets of sequence fragments.