Mastering Python for Bioinformatics

Chapter 7. Translating mRNA into Protein: More Functional Programming

According to the Central Dogma of molecular biology, DNA makes mRNA, and mRNA makes protein. In Chapter 2, I showed how to transcribe DNA to mRNA, so now it’s time to translate mRNA into protein sequences. As described on the Rosalind PROT page, I now need to write a program that accepts a string of mRNA and produces an amino acid sequence. I will show several solutions using lists, for loops, list comprehensions, dictionaries, and higher-order functions, but I confess I’ll end with a Biopython function. Still, it will be tons of fun.

Mostly I’m going to focus on how to write, test, and compose small functions to create solutions. You’ll learn:

• How to extract codons/k-mers from a sequence using string slices

• How to use a dictionary as a lookup table

• How to translate a for loop into a list comprehension and a map() expression

• How to use the takewhile() and partial() functions

• How to use the Bio.Seq module to translate mRNA into proteins

Getting Started

You will need to work in the 07_prot directory for this exercise. I recommend you begin by copying the first solution to prot.py and asking for the usage:

$ cp solution1_for.py prot.py
$ ./prot.py -h
usage: prot.py [-h] RNA

Translate RNA to proteins

positional arguments:
  RNA         RNA sequence

optional arguments:
  -h, --help  show this help message and exit

The program requires an RNA sequence as a single positional argument. From here on, I’ll use the term ...