REVISION EXERCISES 1

These are some revision exercises on sequence statistics and sequence databases.

Exercises

Answer the following questions. For each question, please record your answer, and what you did/typed to get this answer.

Model answers to the exercises are given in Answers to Revision Exercises 1.

Q1.

What is the length of (total number of base-pairs in) the Schistosoma mansoni mitochondrial genome (NCBI accession NC_002545), and how many As, Cs, Gs and Ts does it contain?

You must search for this sequence via the NCBI website, as it is not present in the ACNUC database. Note: Schistmosoma mansoni is a parasitic worm that is responsible for causing schistosomiasis, which is classified by the WHO as a neglected tropical disease.

Q2.

What is the length of the Brugia malayi mitochondrial genome (NCBI accession NC_004298), and how many As, Cs, Gs and Ts does it contain?

You must search for this sequence via the NCBI website, as it is not present in the ACNUC database. Note: Brugia malayi is a parasitic worm responsible for causing lymphatic filariasis, which is classified by the WHO as a neglected tropical disease.

Q3.

What is the probability of the Brugia malayi mitochondrial genome sequence (NCBI accession NC_004298), according to a multinomial model in which the probabilities of As, Cs, Gs and Ts (pA, pC, pG, and pT) are set equal to the fraction of As, Cs, Gs and Ts in the Schistosoma mansoni mitochondrial genome?

Q4.

What are the top three most frequent 4-bp words (4-mers) in the genome of the bacterium Chlamydia trachomatis strain D/UW-3/CX (NCBI accession NC_000117), and how many times do they occur in its sequence?

Note: Chlamydia trachomatis is a bacterium responsible for trachoma, which is classified by the WHO as a neglected tropical disease.

Q5.

Write an R function to generate a random DNA sequence that is n letters long (that is, n bases long) using a multinomial model in which the probabilities pA, pC, pG, and pT are set equal to the fraction of As, Cs, Gs and Ts in the Schistosoma mansoni mitochondrial genome (here pA stands for the probability of As, pC is the probability of Cs, etc.)

Hint: look at the help page for the “sample()” function in R, as it might be useful to use within your R function.

Q6.

Give an example of using your function from Q5 to calculate a random sequence that is 20 letters long, using a multinomial model with pA =0.28, pC =0.21, pG =0.22, and pT =0.29.

Q7.

How many protein sequences from rabies virus are there in the NCBI Protein database?

You must search for these sequences via the NCBI website, as it’s not possible to do this search using SeqinR. Note: rabies virus is the virus responsible for rabies, which is classified by the WHO as a neglected tropical disease.

Q8.

What is the NCBI accession for the Mokola virus genome?

Note: Mokola virus and rabies virus are closely related viruses that both belong to a group of viruses called the Lyssaviruses. Mokola virus causes a rabies-like infection in mammals including humans.

Contact

I will be grateful if you will send me (Avril Coghlan) corrections or suggestions for improvements to my email address alc@sanger.ac.uk

License

The content in this book is licensed under a Creative Commons Attribution 3.0 License.