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.

9 comments:

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.

Kunal

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.

Paolo

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.

milf said...

dessicant air dryerpediatric asthmaasthma specialistasthma children specialistcarpet cleaning dallas txcarpet cleaners dallascarpet cleaning dallas

vero beach vacationvero beach vacationsbeach vacation homes veroms beach vacationsms beach vacationms beach condosmaui beach vacationmaui beach vacationsmaui beach clubbeach vacationsyour beach vacationscheap beach vacations

bob hairstylebob haircutsbob layeredpob hairstylebobbedclassic bobCare for Curly HairTips for Curly Haircurly hair12r 22.5 best pricetires truck bustires 12r 22.5

washington new housenew house houstonnew house san antonionew house ventura

milf said...

new houston house houston house txstains removal dyestains removal clothesstains removalteeth whiteningteeth whiteningbright teeth

jennifer grey nosejennifer nose jobscalebrities nose jobsWomen with Big NosesWomen hairstylesBig Nose Women, hairstyles

milf said...

black mold exposureblack mold symptoms of exposurewrought iron garden gatesiron garden gates find them herefine thin hair hairstylessearch hair styles for fine thin hairnight vision binocularsbuy night vision binocularslipitor reactionslipitor allergic reactionsluxury beach resort in the philippines

afordable beach resorts in the philippineshomeopathy for eczema.baby eczema.save big with great mineral makeup bargainsmineral makeup wholesalersprodam iphone Apple prodam iphone prahacect iphone manualmanual for P 168 iphonefero 52 binocularsnight vision Fero 52 binocularsThe best night vision binoculars here

night vision binoculars bargainsfree photo albums computer programsfree software to make photo albumsfree tax formsprintable tax forms for free craftmatic air bedcraftmatic air bed adjustable info hereboyd air bedboyd night air bed lowest price

milf said...

find air beds in wisconsinbest air beds in wisconsincloud air beds

best cloud inflatable air bedssealy air beds portableportables air bedsrv luggage racksaluminum made rv luggage racksair bed raisedbest form raised air bedsbed air informercialsbest informercials bed airmattress sized air beds

bestair bed mattress antique doorknobsantique doorknob identification tipsdvd player troubleshootingtroubleshooting with the dvd playerflat panel television lcd vs plasmaflat panel lcd television versus plasma pic the bestadjustable bed air foam The best bed air foam

hoof prints antique equestrian printsantique hoof prints equestrian printsBuy air bedadjustablebuy the best adjustable air bedsair beds canadian storesCanadian stores for air beds

migraine causemigraine treatments floridaflorida headache clinicdrying dessicantair drying dessicant