Homework

1. Write an Entrez query to get all 16S nucleotide sequences from E.coli with length at least 1400 basepairs.

2. Write an Entrez query to get all complete Globin protein sequences. The sequence length should be between 200 and 1000 amino acids. The title should not contain the words “partial” nor “domain-containing”.

3. Make a Hamming distance calculator in Excel or Google Sheets.

4. How many comparisons do you need to calculate the Hamming distance between all genetic codes?

5. Prepare a DotPlot in Excel or Google Sheets. Use it to compare the following sequences.

   • ABCDEFGHIJKLMNOPQRSUTUVWXYZ
   • ABCDEAFGNIJKLOPQRSYTUVWXXZ

6. Use the previous answer to find the Levenstein distance between the two sequences.

Mathematical definition of “distance”

(This part is optional, it is useful in life, but it is not necessary for this course.)

Distance is a function taking pairs of objects and returning a number. It is the length of the shortest path between two points.

Notice that the “shortest path” depends on what are the allowed movements. For instance, what is the distance between our campus and Taxim square?

• If we can fly, like a bird or a drone, then the shortest path is a straight line. This is called Euclidean distance, because it is based on the classic geometry described 2300 years ago by Euclid.

• If we have to walk, we must move through the streets. When the city is organized like the Manhattan island in New York, this is called Manhattan distance. (This is not true in European cities). This distance is often used in biology.

• If we take the metro, we will probably count the number of stations we need to cross. The metro is a network, so this is a network distance.

To be a distance, a function \(d\) needs to obey the following rules

• \(d(x,y)≥0\) for all \(x,y\)
• \(d(x,x)=0\) for all \(x\)
• if \(d(x,y) = 0\) then \(x=y\) (we say that \(d\) is reflexive)
• \(d(x,y) = d(y,x)\) for all \(x,y\) (we say that \(d\) is symmetric)
• \(d(x,y) + d(y,z) ≥ d(x,z)\) (this is called triangular inequality)