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LAB Computational Biology Pro

Genome Detective

Investigate an unknown stretch of genome like a bioinformatician, from locating where replication starts to finding genes, hidden signals and CpG islands.

Advanced 6 stages ~6h Python notebook

The brief

You have been handed a newly assembled stretch of bacterial genome and one question: what is in here? Genomes are far too long to read by eye, so biologists write algorithms that hunt for the signals hidden in the sequence.

This lab is one investigation in six stages. You locate the likely origin of replication, search it for repeated control signals, find the genes, search for a signal that tolerates mutations, discover an unknown motif across several sequences and finish by labelling every position of a sequence as CpG island or not with a hidden Markov model. Each stage uses a classic computational-biology algorithm that you may already have met in the problem bank.

WHAT YOU WILL BUILD

A genome-investigation toolkit: a GC-skew scanner, a k-mer frequency finder, a six-frame gene finder, an approximate pattern matcher, a greedy motif finder and a Viterbi decoder for a two-state HMM.

How a lab works

  1. Read the stage brief and look at the given input.
  2. Write code in a notebook that runs on your own computer, using skills from the problem bank.
  3. Submit your code and explanation. We re-run the code on our server against hidden tests, so the result can be trusted.
  4. Check your understanding with a few questions (a self-check in your browser) and explain your approach in your own words.
  5. Finish every stage and the lab is marked completed.

What you'll learn

  • Use simple statistics of a sequence (GC skew, k-mer counts) to locate biological features
  • Find candidate genes by reading a sequence in all six reading frames
  • Search for patterns that allow mismatches, the way real regulatory signals behave
  • Apply a greedy algorithm with pseudocounts to discover a motif nobody told you about
  • Decode a hidden state path with the Viterbi algorithm

Skills from the problem bank

This project builds on techniques practised in these problems. Solving them first is recommended, not required.

The stages

6 stages · ~6h

  1. Find the origin of replication

    Unlock this lab with Pro to open the brief and the notebook for this stage.

  2. Hunt for repeated signals

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  3. Find the genes

    Unlock this lab with Pro to open the brief and the notebook for this stage.

  4. Search with mismatches

    Unlock this lab with Pro to open the brief and the notebook for this stage.

  5. Discover a motif from scratch

    Unlock this lab with Pro to open the brief and the notebook for this stage.

  6. Capstone: find CpG islands with an HMM

    Unlock this lab with Pro to open the brief and the notebook for this stage.