Biopython training course index


Biopython training course prepared by Gen Kaneko.

How to use Repl.it

Basic features:

  1. You can add/remove files and folders from the "Files" section.
  2. Scripts written in main.py will be executed when you hit "Run."
  3. Download Fasta_download.py from this link.

Week 3 Mission


You have the same mision in Blackboard. Turn in from Blackboard.

Here are 10 protein sequences of preproinsulin. Align them and find out the potential C peptide region.

AAR13049.1, AAA41442.1, XP_017214511.2, XP_031158416.1, XP_035798787.1, XP_035798786.1, XP_006781789.1, XP_035525442.1, XP_034739637.1, XP_034545853.1


Week 4 Mission


  1. Download blast.py and Unknown.fasta.
  2. Upload these files to your Repl.it page.
  3. Run Biopython BLAST to identify the sequence in the Unknown.fasta file.
  4. From Blackboard, turn in the name of the gene and its GenBank accession number.

Week 7 Mission


  1. Download GetORF.py and Mission_7.txt.
  2. Upload these files to your Repl.it page.
  3. Modify GetORF.py and find the longest ORF in the sequence in Mission_7.txt.
  4. From Blackboard, turn in the full-length sequence of the longest ORF.

Week 9 Mission


  1. Download MA_plot.py and Mission_9_dataset.csv.
  2. Upload these files to your Repl.it page.
  3. Install the bioinfokit in your Repl.it.
  4. Execute MA_plot.py.

From Blackboard, turn in the MA plot you made. Also briefly explain the difference between Excel file and CSV file using two keywords: "text file" and "binary file". Which one would be more convenient in bioinformatics?

See MA plot to visualize gene expression data using Python for details.

Week 10 Mission


We will use the Breast Cancer Wisconsin (Diagnostic) Data Set for the cluster analysis.

  1. Download Seaborn_cluster.py.
  2. Execute the script in Repl.it.
  3. Prepare a Word file for Mission 10 according to the instruction.
  4. Turn in the Word file from Blackboard.

Week 13 Mission


This week, we will construct a phylogenetic tree using Biopython.

  1. Download tree_example.fasta that contains alignment.
  2. Download tree.py, a Python script to construct a tree.
  3. Execute tree.py in Repl.it.
  4. The font looks too small – modify the scrip to make the font readable.
  5. Turn in the png file of the phylogenetic tree with appropriate font size.

The original script was taken from this StackExchange page. You can further modify the script based on the instruction in this page.








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