Mastering Python for Bioinformatics

Chapter 8. Find a Motif in DNA: Exploring Sequence Similarity

In the Rosalind SUBS challenge, I’ll be searching for any occurrences of one sequence inside another. A shared subsequence might represent a conserved element such as a marker, gene, or regulatory sequence. Conserved sequences between two organisms might suggest some inherited or convergent trait. I’ll explore how to write a solution using the str (string) class in Python and will compare strings to lists. Then I’ll explore how to express these ideas using higher-order functions and will continue the discussion of k-mers I started in Chapter 7. Finally, I’ll show how regular expressions can find patterns and will point out problems with overlapping matches.

In this chapter, I’ll demonstrate:

• How to use str.find(), str.index(), and string slices

• How to use sets to create unique collections of elements

• How to combine higher-order functions

• How to find subsequences using k-mers

• How to find possibly overlapping sequences using regular expressions

Getting Started

The code and tests for this chapter are in 08_subs. I suggest you start by copying the first solution to the program subs.py and requesting help:

$ cd 08_subs/
$ cp solution1_str_find.py subs.py
$ ./subs.py -h
usage: subs.py [-h] seq subseq

Find subsequences

positional arguments:
  seq         Sequence
  subseq      subsequence

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

The program should report the starting locations where the subsequence can be ...