CW 28 — Jul 09
Section outline
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semester overview & summary
- what is computational thinking
- how do biologists search, how do computer scientists search?
- how do we search for patterns?
- how to write your approach as pseudocode?
- which algorithms are better than the others?
- how do we calculate the runtime complexity of algorithms?
- what is a DnaA box?
- what is the motivation behind skew diagrams?
- how to write an algorithm iteratively and recursively?
- what are motifs?
- how do we search for motifs?
- what is a profile matrix?
- what is the difference between count- and entropy-based score?
- what is a median string?
- what are the four algorithms we used for motif search? What are the differences?
- what is the analogy between an exploded newspaper and genome assembly?
- how do we use graphs to assemble a genome?
- what are the differences between overlap and de Bruijn graphs?
- what is an Eulerian graph?
- what is en Eulerian cycle?
- what is the advantage of read-pairs?
- what are the challenges of real sequencing data? How can we overcome them?