Programming problems (biology) - 1
Problem Set – Introduction to Programming (Biology)
1. Why are genome sizes different?
a. What is the length of the genome of Prochlorococcus marinus ss120 (ss120)? How about
the genome of Synechocystis PCC 6803 (S6803)?
For the following, it might be helpful to think of a genome as consisting of coding regions
(the genes) and the sequences in between (the intergenic sequences).
b. Does S6803 have more genes than ss120?
c. Does S6803 have bigger genes than ss120?
d. Does S6803 have bigger intergenic sequences than ss120?
e. Summarize what you've found. Why are the genome sizes different?
2. Sequences of genomes, genes, and proteins
a. Display the first 2000 nucleotides of the ss120. Not very illuminating!
b. Copy the display into a word processor and modify it by highlighting to make evident
where are the genes in this region of the chromosome and where are the intergenic
sequences. You may find helpful the FROM and TO keywords in the GENES-OF
function and the View command on a result's Action menu.
c. Do the same with the ss120 chromosome from 9000 to 11000. How might you account
for the differences between these two regions?
d. Display the same two regions, this time using READING-FRAMES-OF (obtainable
through either the All menu or the Genes-Proteins menu, Translation submenu). Note in
this display where your genes begin and end.
e. Display the amino acid sequence for the proteins encoded by the first gene identified in
6a and in 6c. DISPLAY-SEQUENCE-OF will work for protein as well as genes, and to
get the protein, you can use the PROTEIN-OF function (Genes-Proteins menu) or simply
enter the gene's nickname (the part to the right of the decimal) preceded by "p-".
f. Compare the amino acid sequences of the two genes to
3. Codons and amino acids
Take a look at a table showing the codons and the amino acids they encode. You'll see that
some amino acids are encoded by several codons, others by only one. Why is that? Consider
the simple hypothesis that there is a correlation between the number of codons that encode an
amino acid and how common that amino acid is in proteins. Are serine and leucine, with 6
codons apiece, 6-times more common than tryptophan and methionine, with only 1 codon
apiece? Find out, using as a test the coding genes of the organism Prochlorococcus marinus
ss120.
a. What information do you need to know in order to answer this question?
b. What kinds of functions do you need in order to gather that information?
