CW 28 — Jul 09

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?