Bioinformatics Class Fall 2015

My favorite online Python books

You must be coming from a Truman IP address (meaning using a computer on campus or running VPN software from off campus) to access the full text of these books.

Learning Python by Mark Lutz. This assumes are somewhat familiar with programming and teaches Python.

Introducing Python by Bill Lubanovic. This is even more introductory than the above, and has lots of hands-on examples.

Homework

• Homework 0 for Biology students
• rnatest.py and sasquatch.fasta are files that can help you test your solution to the last question. The rnatest file uses the sasquatch data to compare sasquatch DNA to the RNA sequence that your code generates and tells you if you got it right or not.

Getting Started with Python

• Lab 0 from last time I taught CS 170. You are NOT required to complete this lab, but it takes you through the process of using Python in the Truman environment.

Regular Expressions

• HOWTO Regular Expressions is part of the Python documentation that focuses on regular expressions.

FASTA format

• Wikipedia has a nice detailed description of the FASTA format.

Links to useful Python files

• countt.py
• readfasta.py
• filestuff.py
• geneticcode.py
• rna2aaALMOSTWORKS.py
• translate.py
• maizefragment.fasta