Pin Me

Why PERL for bioinformatics?

written by: Finn Orfano • edited by: Leigh A. Zaykoski • updated: 5/16/2008

PERL is used in bioinformatics because of its ability to run on all operating platforms, is flexible to handle, modify, add modules easily in one simple language, and output in a format desired by the user.

  • slide 1 of 1

    PERL is the acronym for  Practical Extraction Reporting Language. It is the main language used in bioinformatics.

    Why is PERL used? We use PERL because it is very easy to learn and enables working with functions that are powerful with text: search, extract, modify and combine. Not to mention, PERL is free and works on all operating systems. It also has many pre-built modules that are available that enable researchers to do many useful things.

    PERL is used for bioinformatics for reporting and parsing files. Many programmers use this language for developing online tools because it easily combines with HTML and ASP. Another important feature of PERL is that it is very strong language for handling text files. Most of the bioinformatics tools use text file for saving the output. So, they can be very easily handled in PERL. There are many string modification functions in PERL which perform many useful tasks.

    Another main and important use of PERL in bioinformatics is pattern matching. In bioinformatics, main research is done on a particular sequence. At this point pattern matching of PERL is very much useful for finding, modifying, matching, and translating a string or substring in the main string. A substring can be extracted from the main string and any given pattern can be easily extracted.

    PERL is also good in manipulation of arrays. They handle the strings in arrays (if we want them to) and many array manipulation functions are present for modifying data stored in arrays. Because of this, PERL is used as the main programming language for bioinformatics. PERL is strong at handling strings and text files. Here is where it helps as bioinformatics also deals with strings and uses text files.

    The most important feature of PERL is its portability and availability on all operating platforms. Software programmers know how difficult it is to transit from one operating system to another. PERL is a great benefit to them.