Tuesday, April 8, 2008

Why PERL makes life easy for Bioinformaticians ?

Plz Visit 123Bioinformatics.com for more Updates.

1. Perl Scripts are very easy for the String processing when using biological data like Genome sequences or protein sequences.

2. File handling is easy in Perl.

3. Perl regular expression is very flexible and easy to match similar patters rather than identical ones. It can be used in instance like matching a motif or a repeat in a sequence.

4. There are no strict rules for writing Perl scripts like other languages. That makes it easy for the biologist to learn Perl in short period.

5. Perl scripts can be combined with SHELL scripts for text processing.

6. Using Perl CGI and HTML one can develop the Web pages. Perl CGI is very similar to Perl scripts.

7. CPAN contains hundreds of Perl Modules which are Specific for sequence analysis.
Eg: FASTAParse , Peptide::Pubmed .

8. Perl can be used for System administration purpose also.

9. Perl Template tool kit is another Perl product which can be used for developing advanced web pages.

10. Using perl DBIx it is easier to pass mysql data (backend) to the web page(front end).

11. Processing / Parsing a HTML file is very easy by using CPAN modules.

12. File type conversion is possible in Perl using CPAN modules. Ex:Doc to PDF ,HTML to PDF ..Etc.

13. By using Perl Magick module we can do image processing.

14. Perl critic module will help you to write a best Perl codes by criticizing your code structure.


Settu Sridhar said...

nice info..perl critic will be really usefull..thanks

nicks.den said...

As the saying goes:

"Perl is best for biology, because its as sticky as complex biology is".

Perl is also called a glue language. It is widely used for development of automated pipelines for genome data annotation, high through put screening etc as it has commands like system, backticks etc which are used to combine various process into a single pipeline.


pr said...

It would be nice to see similar reasons for other languages, I'm sure there are.
Languages war is a never ending topic, we can discuss forever.
The problem is that people is different, as are languages different.
All language has its strength and weaknesses, its best and worst scope, and each person has his/her attitudes.
So, the best starting doc would consist in a commented list of best scopes for all languages.

Linked to this topic, I see the problem of 'good bioinformatics programming practice', that relates to scopes, libraries/modules, open source and reuse. But this is another story.


azalea said...

All you said is valid if you replace 'Perl' with 'Python' :) no language war intended..
I agree with pr that every programming language has pros and cons, it is really helpful to compare the best features of each language and let bioinformaticians make their choice.

Anonymous said...

HTML::Mason can be used to develop webpages with Perl.

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