Chapter 13. Location Restriction Sites: Using, Testing, and Sharing Code

A palindromic sequence in DNA is one in which the 5’ to 3’ base pair sequence is identical on both strands. For example, Figure 13-1 shows that the reverse complement of the DNA sequence GCATGC is the sequence itself.

mpfb 1301
Figure 13-1. A reverse palindrome is equal to its reverse complement

I can verify this in code:

>>> from Bio import Seq
>>> seq = 'GCATGC'
>>> Seq.reverse_complement(seq) == seq

As described in the Rosalind REVP challenge, restriction enzymes recognize and cut within specific palindromic sequences of DNA known as restriction sites. They typically have a length of between 4 and 12 nucleotides. The goal of this exercise is to find the locations in a DNA sequence of every putative restriction enzyme. The code to solve this problem could be massively complicated, but a clear understanding of some functional programming techniques helps to create a short, elegant solution. I will explore map(), zip(), and enumerate() as well as many small, tested functions.

You will learn:

  • How to find a reverse palindrome

  • How to create modules to share common functions

  • About the PYTHONPATH environment variable

Getting Started

The code and tests for this exercise are in the 13_revp directory. Start by copying a solution to the program

$ cd 13_revp $ cp ...

Get Mastering Python for Bioinformatics now with the O’Reilly learning platform.

O’Reilly members experience books, live events, courses curated by job role, and more from O’Reilly and nearly 200 top publishers.