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Using PERL for Bioinformatics

written by: Finn Orfano • edited by: Leigh A. Zaykoski • updated: 6/19/2008

This article discusses the specific strengths and features of the programming language Perl. More specifically, it explains PERL’s usefulness in the field of bioinformatics.

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    PERL is a programming language created by Larry Wall. PERL stands for Practical Extraction and Reporting Language. This language has gained a lot of importance in the last few years, and is now very widely used for different tasks. It is used in aeronautics, engineering, and bioinformatics.

     
    The main feature of Perl is its simplicity and ease of use. The basic syntax of Perl is its main strength. The syntax of Perl is very simple and easily understood by the user. Perl also has interoperability with other programming languages. It can be embedded in any other programming language without much difficulty. It also has a very sophisticated type system.

     
    Perl programming language is a unique programming language when compared to other programming languages. It is basically a natural language. Perl is a free, open source programming language. Perl is excellent for text processing, sequence analysis, data mining, data management, and web development. It is a general purpose and a powerful language. Yet, it is highly suitable for writing useful programs.

     
    Perl is both a compiled and interpreted language. The errors are compiled automatically. No manual compiling is required. It is a free format language. It can add free new spaces, tabs, or lines whenever and wherever needed in the program. Perl is used in text processing because it is easy to extract relevant information from text files written in a certain format, analyze and modify the extracted information, and store information and display that information.

     

    Perl is said to be the ideal language for biological data analysis. Perl is preferred in the bioinformatics field because it has certain really nice features, such as string processing, CGI programming, it is easy to learn and write, the availability of modules for bioinformatics, and it is fast and suitable for writing short programs instead of large codes. Therefore, Perl is used in bioinformatics because it has simple and powerful features. It is the best programming language for analyzing biological data.

    Interested in learning more about Perl? Read these articles:

    Using Regular Expression in Perl

    Perl CGI and Web Programming