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Lecture 08

For our next set of lectures, we'll use Python to explore some specific tools common in computational biology research. Lecture 08 and 09 from Maggie Russell will introduce you to the use of packages in general, and Biopython in particular, which includes many useful tools for manipulation and analysis of data related to molecular biology. We've included a number of practice exercises in this section to help you gauge your understanding of the material.

Learning objectives

After this section, you should be able to write Python functions that perform some useful real biological analyses:

  • Get the reverse complement of a sequence (learn to use a Python dict).

  • See if a sequence matches using ambiguous nucleotides (learn to use the Python re module).

  • Parse barcodes from a real deep-sequencing experiment (learn to use biopython).

Class materials

  • The content for this lecture is contained in the Jupyter notebook lecture08.ipynb located in this directory.

  • All of the necessary packages should already be installed within the class Docker container

Reminders

  • Homework 4 will be finalized by end-of-class on October 26th and will be due on November 2nd