Perl for Bioinformatics.

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CPAN offers two command-line utility modules. Perl-Tidy module to beautify, indent, and reformat a messy Perl script and Perl-Critic module to test/analyze Perl scripts.

a. Perl::Tidy
When a Perl script is given as an input to perltidy, it creates a intended, structured Perl script and saves it as a separate file using the same name but with a .ty extension. Perltidy does not change the input script.

Steps to follow,
1. Install Perl::Tidy. It can be run on any system with perl 5.004 or later and used on Unix, Windows, VMS and MacPerl.
2. To execute perltidy,
$ perltidy -[option] test_perl_script.pl
This will create a temporary file test_perl_.pl.ty. The test_perl_script.pl .ty file will contain the well structured perl script. There are many options that can be used indent, to take a back-up etc. For more information on installation and execution see, http://perltidy.sourceforge.net/tutorial.html


b. Perl::Critic

Perl-Critic criticizes/analyses the input Perl script and enforces the user to follow various coding guidelines (or policies). The coding guidelines are based on Damian Conway's book Perl Best Practices. The user can enable/disable or create and customize the modules through the Perl::Critic interface.
The user can set the severity levels. There are 5 severity levels: severity "5" is the most or least restrictive level ie Perl::Critic follow the basic policies/guidelines. The five levels are Gentle (equivalent to 5), stern (equivalent to 4), harsh (equivalent to 3), cruel (equivalent to 2), brutal (equivalent to 1).
Perl::Critic requires a few modules to be pre-installed for it to execute. See http://search.cpan.org/~elliotjs/Perl-Critic-1.082/lib/Perl/Critic.pm


Steps to follow,
1. Install Perl::Critic.
2. Execute Perl::Critic
$ perlcritic –1 test_perl_script.pl

For more information see, http://search.cpan.org/dist/Perl-Critic/

Why PERL makes life easy for Bioinformaticians ?

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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.

What is Bioinformatics

What is bioinformatics ?

It's method to predict the biological outcomes before anyone go for full fledged research. It's a method to compare the biological data. Ex: sequence analysis. It's a way to predict or solve the protein structure.
It's the only way for PERSONALIZED MEDICINE in this post genomic era. It's the method to do comparative genomics and predict the Human homolog genes in other species.
It's the method to annotate the newly sequenced genomes.

How the biological problems can be predicted ?

We are living in the world of Computers. By analyzing the existing biological data using Information Technology we can predict the biological outcomes.

What is the HOTTEST branch of Bioinformaics in this post genomic era ?

Personalized medicine is the most hottest and fastest growing field. Personalized medicine can be achieved through bioinformatics only.

Genetic Genealogy or Ancestry

Genetic Genealogy is one of the very interesting and successful commercial field in Bioinformatics and Genetics. Based on the Genetic markers of an individual, researchers came up with an idea to predict the genealogy or ancestry of the individual.

There are two types of Ancestry prediction. One is Maternal and the second one is paternal. Maternal ancestry prediction is based on Mitochondrial Genetic Markers(SNPs). That will tell the story of your ancestors and the migration path they took from Africa. Paternal ancestry prediction is based on Y chromosome STRs.

100,000 Years before the First Human called Eve lived in Africa near Ethiopia. she belongs to the Haplogroup called L0. Descendants of L0 called L3 who are the first people came out of Africa to explore the new world 60,000 years before. First they reached Middle eastern part. Then some of the people came to Europe and Asia. Some of the people belong to Haplogrop A crossed Siberia and reached America 10,000 - 20,000 years before. Genography project has defined the Markers for each haplogroups. There are so many companies for the Ancestry prediction.

Learn More
1. Haplogroups.
2. Maternal Ancestry.
3. Paternal Ancestry.

Job opportunities in Bioinformatics

When we think about Job or Research after a degree in Bioinformatics, most of the people choose to do Ph.d in US and Europe.

Most of the European Universities prefer the students who are really interested in doing research for 3 - 4 years. Most of the universities don't expect TOEFL to apply for Ph.d.

American universities chose based on GRE and TOEFL scores to do Phd for 5 years.

Finally companies prefer the students who are strong in software side.