| exhaustive search / branch-and-bound and motif finding |
some programming skills |
can explain what motif finding is and program an exhaustive algorithm for it |
learns how to use the techniques in the context (e.g. motif finding) studied at the course |
can apply branch-and-bound techniques to new problems in bioinformatics |
| greedy algorithms and genome rearrangements |
some mathematical thinking |
understands how permutation sorting is connected to genome comparison, and can simulate a greedy algorithm for sorting by reversals |
learns how to use the technique and approximation analysis in the context (e.g. genome rearrangements, shortest superstring) studied at the course |
can apply greedy algorithms and their analyses to new problems in bioinformatics |
| dynamic programming, sequence alignment, and sequence-based phylogeny |
some mathematical thinking |
can manually fill a dynamic programming matrix given the recurrence |
learns the idea of computing sequence alignments and sequence-based phylogenetic trees by dynamic programming |
can develop new dynamic programming algorithms for different variants of sequence alignment and analysis problems |
| graph algorithms and DNA sequencing |
some mathematical thinking |
can simulate one of the reductions to graph problem studied at the course |
learns the connections of graph algorithms to DNA sequencing (e.g. sequencing by hybridization, interval graphs, shortest superstring) |
can reduce new bioinformatics problems to problems on graphs |
| clustering and phylogeny |
some mathematical thinking |
can simulate a clustering algorithm for distance-based phylogeny |
learns UPGMA and neighbor joining clustering algorithms and their connection to distance-based phylogeny |
can prove theorems on neigbor joining analysis |
| Python programming |
some programming skills |
can modify a given simple Python program to do something similar |
learns the basics of Python in order to solve simple script-like programming exercises |
turns easily any algorithm pseudocode into Python code |