Using Regular Expression in PERL — The Preferred Programming Language for Bioinformatics

Before understanding how to use regular
expression in bioinformatics, one must first have an understanding of what
regular expressions are. Regular expressions are a way of describing a pattern.
Creating a pattern is an interesting feature of Perl. In some cases, we use the
same character to create a pattern, or for testing a pattern. However, in Perl
we can also use some special symbols known as meta-characters. Meta characters indicate a group of similar characters or
that match a special position in a string.

Regular expressions are mainly used to
match, substitute or translate characters. Without these regular expressions,
Perl would be a fast developPerl CGI and Web Programmingment environment. Mainly regular expressions are
used for string comparisons.

Regular expressions in Perl have three
important operators: the match operator, the substitution operator, and the
transliteration operator. The match operator is used to match a string if a
particular pattern is present or not. If that pattern is present, then it will
return true, and if it is not present, then it returns false. So, the main
function of the match operator is to match the given pattern of a string. The
substitution operator is used to substitute the pattern with another given
pattern. It is mainly used to substitute one letter, or one string, with
another letter or string. The transliteration operator is used to transliterate,
or translate, the text or strings present in a file.

These operators are used for managing
biological data. For example, translation is done by replacing A with U, G with
C, and T with A and C with G. This is possible with the transliteration
operator. This operator is used to translate the given text with the other.

Sometimes, these operators are used to find
the restriction sites. Here, the match operator is used to find the presence of
restriction patterns. Therefore, regular expressions play an important role in
solving different biological problems.

Interested in learning more about Perl? Read these articles:

Perl CGI and Web Programming

Using Perl for Bioinformatics