The best Bioinformatics programming language
ADVERTISEMENTS
The best Bioinformatics programming language
As you now, bioinformatics is the use of computer hardware and software to analyze or interpret biological data, most of bioinformaticiens use ready programmed softwares, and most of these softwares can give you what you exactly want.
But lets say that you want to extract some specific data from database files for example, what will you do than.
Bioinformatics softwares are made or programmed by specialists in the programming field using programming languages (c, c++, perl, phython, java...etc), i'm not saying that you have to learn them all, but PERL (Practical Extraction and Report Language), is the most powerful and ideal in Bioinformatics.
Why exactly PERL:
You may say that we have a lot of programming languages choices, why PERL, well we have already seen bioinformatics programs written in other languages such as (c, java, phython, FORTRAN...etc), but PERL is the best in the field because it can highly detects data patterns especially what we call STRINGs of text, so PERL is the best programming language for bioinformatics.
We mean by STRINGs characters of DNA/RNA or protein sequences (ATGATCCAGT for example).
I found this OREILLY book 'Beginning PERL For Bioinformatics' very helpful, and i advise that you read it to understand better how to design your own programs that are suited to your needs instead of using others programs.
Any question, comment.
Posts
4 comments:
use the right regular expression library and you have pattern detection capabilities in ANY of those languages
You are absolutely right, but in my experience, PERL is the easiest and the most efficient one. It's installed in almost all Linux distributions and you can install it in windows if you want. With the addition of BioPERL and it's magnificent libraries, you'll become an invincible Bioinformatician!!!, thanks for the comment and good luck.
It would have been nice if you could have compared the different languages you mentioned for each of their merits so that the reader could have made up his/her own mind. Especially since there is also BioPython, BioJava, and BioRuby so the point about BioPerl is less impressive.
Besides, each language has it's own merits and flaws, so it largely depends on the application as to which language you choose.
You are absolutely right, each of the programming languages has its own advantages and disadvantages, i'm just suggesting that PERL is a very good programming language especially for beginners, may be in an other post i'll explain in details the advantages and disadvantages of using each programming language in Bioinformatics.
Post a Comment