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Problem set

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Problem set#

Overview#

A set of problems will be handed out on Friday, 20.02.2026. The solutions to the problems must be submitted through Moodle by Thursday, 19.03.2026. After initial assessment, students with insufficient answers will receive an additional chance to revisit and correct their work until Thursday, 26.03.2026. You should submit your solutions on moodle:Moodle

Most of the solutions will be similar to those of in-class problems we have been solving each week or can be found by starting from those exercises. We do not want anyone to struggle for a long time trying to get something to work, so please use the usual channels to seek help when you are stuck or otherwise need help:

Part 1#

Problem scenario: The research expedition Tara Pacific sampled microbial communities in the ocean and coral reefs across the Pacific Ocean. You would like to collect some basic statistics about the project, such as: ‘How many and what kind of samples were collected?’ The following problems will test your ability to solve these questions using the command line interface and by executing basic commands.

Tara Oceans foundation Tara Pacific expedition

Question 1

Using the command line interface, connect to the server “lovelace.ethz.ch” and create in your home directory a new directory named problem_set and two sub-directories, one named script and another one named results.

Question 2

In your problem_set directory, download from the internet the metadata file for the oceanic research voyage Tara Pacific. https://zenodo.org/records/6299409/files/TARA-PACIFIC_samples-provenance_20220131d.tsv

If the above link does not work for you, you can also access the file here:

/nfs/nas22/fs2202/biol_micro_teaching/551-0132-00L/7_Project/TARA-PACIFIC_samples-provenance_20220131d.tsv

Question 3

If examining the column “sample-material_label”, how many samples from “CORAL” were taken? Provide the answer AND the command you used to get your answer.

Question 4

How many unique sample materials (e.g. CORAL, SEDIMENT, FISH, …) are listed under “sample-material_label”?

Question 5

How many samples are listed for each unique sample material? Save the result in the directory results as a file named count_unique_samples.txt.

Question 6

Compress the Tara Pacific metadata file in your problem_set directory. Consult the manual of the command to achieve the best-possible compression.

Now, assume you have isolated a microorganism and would like to find out more about it. You have asked a company to sequence the genome of the microbe and have received the data in FASTA format. The file is named <your ETH username>.GCA*.fasta. Please note: GCA_* is the unique accession identifier that has been assigned to the genome by NCBI/GenBank. The file can be found in the directory /nfs/nas22/fs2202/biol_micro_teaching/551-0132-00L/7_Project/FS26_Genomes/ Begin by copying the genome fasta file to your script directory. Please provide answers to the following questions about your genome.

Question 7

Identify the Genus and Species name of the organism from which your genome came.

Question 8

Count the number of lines and the number of sequence entries in the genome fasta file you were assigned.

Question 9

How many bases are there in the genome you were given? Provide a script named genome_bases.sh in your script folder that will output the number of bases.

Question 10

What is the GC content (in %) of your genome?

For the last two questions, you will need to predict open-reading frames in the genome using a tool called ‘Prodigal’. Prodigal can be loaded from the module system (you will be introduced to this on 27.02.2026).

Question 11

What is the longest open reading frame in the genome?

Question 12

What is the maximum number of times the codon “ATG” occurs in your genome?

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