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 Jesse Bloom 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.
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).
The content for this lecture is contained in the Jupyter notebook lecture08.ipynb located in this directory.
Please install Biopython prior to class by opening Terminal (Mac) or Anaconda Prompt (Windows) and executing the following code: conda install -c anaconda biopython . Alternatively (on either platform), open Anaconda Navigator, go to “Environments” and click “not installed”. Search for biopython click the box to install.
This class requires use of Python 3.6+. If you installed Anaconda recently (e.g., within the last few months, since the start of the course), you should be fine. If you are working with an older installation of Python, please see these instructions for checking your version and updating if necessary.