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4 - Biological Patterns and Regular Expressions

from Part II: - Sequences

Published online by Cambridge University Press:  19 August 2022

Benny Chor  and
Amir Rubinstein
Benny Chor
Affiliation:
Tel-Aviv University
Amir Rubinstein
Affiliation:
Tel-Aviv University
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Summary

In this chapter, we study another common string-related problem – pattern matching. Suppose we want to find a given sequence motif, or pattern, in a genome or protein, where the pattern is not unique. In other words, the pattern has more than a single possible matching sequence. To that end, we will introduce the fundamental notion of regular expressions, and their use to solve this problem. In addition, we will discuss the closely related notion of finite state machines (FSM), another basic concept in computer science.

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Computational Thinking for Life Scientists , pp. 79 - 90
Publisher: Cambridge University Press
Print publication year: 2022

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