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.
piannaf/Median-K-Mer
Optimization of an algorithm for finding the median k-mer of a DNA sequence.
Java