BioPerl Tutorial: Introduction to BioPerl

bioperl tutorialA lot is talked about Perl, BioPerl and their role in Bioinformatics. Thus, I thought to create a BioPerl tutorial series in which I will be enlightening Bioinformaticians about ways in which BioPerl and Perl come to aid of Bioinformaticians.

Why Perl is so popular among Bioinformaticians?

I think all my readers of this blog would know why Perl is popular among Bioinformaticians.  For those who are still bemused, following are couple of reasons:

  1.  Perl is simple to understand and code for Biological students (as most of students in Bioinformatics are from Biological background).
  2. Another reason is availability of various regular expressions which help in handling sequence data better.

Introduction to BioPerl:

BioPerl is nothing but addition of biological (specifically BioInformatics) modules to Perl (existing language).

Importance of BioPerl:

  •  BioPerl modules help in writing perl programs for dealing with sequences in a better manner.
  • BioPerl offers many objects for different sequences (DNA, RNA as well as protein) and annotations associated with them.
  • BioPerl provides interface for sequence analysis with thridy party software like FASTA, BLAST, CLUSTALW and many more.
  • BioPerl modules acts as interface for remote (EMBL and GenBank) as well as local (flat files, MySQL) databases for the purpose of storing and intervening sequences.

Portability:

Though most of Bioinformatics applications are developed in Linux/ UNIX environments but need for Windows based software and programs is growing. BioPerl is one such software which can be installed on Windows as well as most of Unix/Linux Operating Systems. One can write code in BioPerl in windows and it can be executed on Linux system.

Relationship with C, C++

Most of bioinformatics applications were developed originally in languages like C++, C and Pascal (e,g, clustalW, BLAST etc). BioPerl modules act as a wrapper which allows execution as well as retrieval from these external sources.

In the next article on this BioPerl tutorial series, we will see how to install BioPerl in Windows as well as on Linux (Cygwin).

 

About Brij

Bhrat Brij is a SEO expert, Internet Marketer, Affiliate Marketer and Bioinformatician. My short bio or have a look on my Google Profile

Comments

  1. I tried to install bioperl but could not install because when i installed active perl on the third step, i only able to click top two not the third one. Is there any way i can click third (creat .pl script maping for perl) also. thank you so much for your help

    • Hello Amrit,

      Can you let me know which version your are trying to install and your system config? Do you have IIS/XAMPP/WAMP on your system? Then I might be able to help you better.

      Regards,
      Bhrat

  2. Dear Bhrat
    I tried to install in both (32 and 62bits) computer ActivePerl-5.14.2.1402-MSWin32-x86-295342.msi for 64bits and others in 32bits. Thank you.
    with best regards.
    amrit

  3. Dear Bhrat
    I am sorry, i am very new in computer. I don’t know what is IIS and OS mean? Thank you.
    Amrit

    • Amrit, OS is operating system like Windows, Linux and version like Windows 7 home, Windows 7 basic, Windows XP pro, Windows XP home.

      IIS is Internet Information Services. An app used for handling scripts. It creates a virtual server on your system to run those scripts as the last option is for handling scripts (.pl script) which is run on server (IIS).

  4. Dear Bharat
    I am using Windows operating system. Thank you.
    best regards.
    Amrit

    • Amrit do have IIS installed? Again you have not mentioned which version it is. XP basic, XP home, XP pro, Windows 7 ulitmate, Windows 7 basic.

  5. bharti kishnani says:

    i am not able to install bioperl…itz windows xp..the problem i am facing is installation of perl..in dat i am not able to select all the three options only 2 options i am able to select

Trackbacks

  1. […] my last article I covered importance of BioPerl in Bioinformatics and why Perl is popular among Bioinformaticians. This article in this BioPerl […]

  2. […] Tutorial series, we will see how to write BioPerl Program or BioPerl Script. If you are looking for BioPerl Introduction and Usage, click here and to install BioPerl you can see this BioPerl tutorial for windows […]

  3. […] article we will see how to use BioPerl modules, especially SeqIO module. If you are looking for BioPerl Introduction and Usage, click here; to install BioPerl on Windows you can see this BioPerl tutorial and to write your […]

  4. […] Introduction to BioPerl […]

  5. […] my work I found extremely useful the tutorial made by Bhrat Brij that can be found here: BioPerl Tutorial. __spr_config = { pid: '4e3ac111c2b219498d00009c', title: 'BioPerl for bioinformatics', ckw: '', […]

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