CSE 549 Homeworks

Professor: Rob Patro

Course webpage: Computational Biology

Homework 1

• Counting DNA Nucleotides: http://rosalind.info/problems/dna/
• Overlap Graphs: http://rosalind.info/problems/grph/
• Inferring mRNA from Protein: http://rosalind.info/problems/mrna/
• Introduction to Random Strings: http://rosalind.info/problems/prob/
• Translating RNA into Protein: http://rosalind.info/problems/prot/
• RNA Splicing: http://rosalind.info/problems/splc/
• Genome Assembly as Shortest Superstring: http://rosalind.info/problems/long/

Homework 2

• Implement BetterBWMatching: http://rosalind.info/problems/ba9m/
• Construct the Burrows-Wheeler Transform of a String: http://rosalind.info/problems/ba9i/
• Implement BWMatching: http://rosalind.info/problems/ba9l/
• Counting Optimal Alignments: http://rosalind.info/problems/ctea/
• Edit Distance Alignment: http://rosalind.info/problems/edta/
• Generate the Last-to-First Mapping of a String: http://rosalind.info/problems/ba9k/
• Maximizing the Gap Symbols of an Optimal Alignment: http://rosalind.info/problems/mgap/
• Mortal Fibonacci Rabbits: http://rosalind.info/problems/fibd/

Homework 3

• Genome Assembly with Perfect Coverage: http://rosalind.info/problems/pcov/
• Constructing a De Bruijn Graph: http://rosalind.info/problems/dbru/
• Error Correction in Reads: http://rosalind.info/problems/corr/
• Find an Eulerian Path in a Graph: http://rosalind.info/problems/ba3g/
• Implement SmallParsimony: http://rosalind.info/problems/ba7f/