Justin Mancinelli

Complete assignment 2 for COMP3506 at the University of Queensland

Description: Incrementally optimize an algorithm for finding the median k-mer of a DNA sequence.

Pseudo-code was given for a naive implementation so I first implemented
that. Then, I added the branch-and-bound mechanism which significantly
sped things up. Then, I implemented the trie to store k-mers which allowed
me to optimize the algorithm to search promising k-mers first which sped
things up slightly more.

MedianKMer.java has the final two implementations which I benchmarked for
the final report.

Files: benchmark. -- The way I benchmarked the implementations. Results are put into a CSV file for later analysis. motif. -- Classes required for the algorithm. I don't think I changed anything other than MedianKMer.java and TrieKMer.java. 10COMP3506Assignment2.pdf -- The assignment specification. .PNG -- Pivot charts out of Excel .csv -- Results of benchmarking (may not be named correctly) report.* -- The final report.