Regular Expressions for Biologists: Glossary

Regular expressions are a way of describing patterns in text.

Most text editors and many other tools include a regular expression engine for performing these kinds of searches.

Regular expressions are often offered as a mode of find/replace that can be turned on and off by the user.

Wrap characters in [] to define a set of valid matches for a given position.

Use - between two characters to define a range of characters to match.

^ at the start of a set to invert it, indicating that the given characters should be excluded from a match.

Use the  token to match a word boundary, and ^ and $ to match the beginning and end of a line respectively.

\ has special meaning in regular expressions, and \\ should be used to specify a literal backslash in a pattern.

. describes a position that could match any character.

When composing a regular expression, it is good practice to be as specific as possible about what you want to match.

? indicates that the preceding character or set should be treated as optional in this position.

* indicates that the preceding character or set should appear 0 or more times in this position.

+ indicates that the preceding character or set should appear 1 or more times in this position.

{2,4} indicates that the preceding character or set should appear at least twice but no more than four times in this position.

Capture groups are defined within () in a regular expression.

The left-most capture group in a regular expression is referred to with \1 in the replacement string, the next with \2, and so on.

Alternative strings to match can be combined with |.