• Midterm exam review
• Sequence similarity
• Sequence assembly

1. What is Markdown? Why it is useful for Science?
2. What are the elements of a structured document?
3. What are the elements of this document? (the exam itself)
4. Why it is important to separate content from style in a scientific report?

1. What is GEO? Why is it useful for Molecular Biology and Genetics?
2. What is MIAME?

• Which are all the entities?
• What are their relationships? That is, how are they related?
• What are their attributes? Remember that entities and relationships can have attributes
• What are the identifiers?
• What are the cardinalities?

Entity-Relationship Diagram of GEO

1. Why clustering is an useful tool for Molecular Biology and Genetics?
2. What is a distance in hierarchical clustering? Please give examples
3. What is linkage? Please give examples

1. The sequences of amino-acids of a set of proteins
2. The genome of a yeast and the location of its genes
3. The locations in the chromosome of transcription factors binding sites
4. The sequence of a plasmid

1. How do you determine the origin of replication in a bacterial chromosome? Can you do the same in Eukarya? Why?
2. How do you determine the binding sites of a transcription factor?
3. What is a Motif? What is a Position Specific Score Matrix (also known as Position Weight Matrix)?

• Input: list of vector of characters named CDS
• Output: list of vector of characters
• you can use the function translate() that transform a single CDS into the corresponding protein

1. Write first a function score.pos() to evaluate the score of a fixed position. The inputs are
   • pos: position in the genome
   • genome: vector of chars
   • mat: a position specific score matrix
2. Then write the code to evaluate score.pos() on each position of a genome. The final output is a vector of numbers, each one representing the score of each position.

DNA replication is not perfect. Some bases can change

• Substitution of nucleotides
• Insertion
• Deletion

If these changes are lethal, the cell dies (by definition)

Therefore we only see changes that are compatible with cell life

This is one component of natural selection

Naturally, if two genes have the same sequence, they encode the same protein

If they differ in a few bases, the proteins will also differ a little, or less (why?)

So if two proteins are very similar, they probably do the same function

A few changes will probably not change they way it folds

Same shape, same function.

Comparing sequences