Main Page

From Biophp_net

Jump to: navigation, search

openfree BioPHP.Net

PHP is a reflective computer programming language originally designed for producing dynamic web pages.PHP is used mainly in server-side scripting, but can be used from a command line interface or in standalone graphical applications. Textual User Interfaces can also be created using ncurses. PHP is a recursive initialism for PHP: Hypertext Preprocessor.PHP is a widely-used general-purpose scripting language that is especially suited for Web development and can be embedded into HTML.

BioPHP is a package of Open Source PHP code, with classes for DNA and protein sequence analysis, alignment, database parsing, and other Bioinformatics tools.


 Why BioPHP?

PHP or BioPHP  has some important  features that makes it useful in bioinformatics application.These features can also be called as the four-P's of PHP.

  • Practicality

From the very start,the PHP language  was created with practicality in mind.After all,Lerdorf's original intention was not to design an entirely new language,but to resolve a problem that had no readily available solution.Furthermore,much of PHP's early evolution was not the result of the explicit intention to improve the language itself,but rather to increase its utility to the user.The result is minimalist language,both in terms of what is required of the user and in terms of language's syntactical requirements.

For starters, a useful PHP script can consist of as little as one line;unlike C,there is no need for the mandatory inclusion of libraries.For example the code given below output the complete information about PHP installed on the system

  •  Power

 The latest version of PHP has 113 libraries  containing over 1000 functions.PHP has easy connectivity to various database servers and creates dynamic web pages.PHP can  create and manipulate Macromedia flash,image and PDF files.It can also communicatewith a wide variety of protocols,including  IMAP,POP3,NNTP and DNS.

  • Possibility

PHP developers are not bound to a single implementation solution.They have wide possibilities .For example PHP database support itself includes more than 25 database products starting from dBASE,MS SQL to Sybase and Velocis etc. . PHP's powerful string parsing capability has made it on power with scripting languages like Perl,Python.It has more than 85 string manipulation function with both POSIX and perl based regular expession formats.In addition to this PHP offers embraces Object Oriented and functional paradigm.The recurring theme here is that PHP allows you to quickely capitalize on your current skills set with very little time investment.


  • Price

PHP is an opensource product ,therefore since its inception it has been without usage,modification and redistribution restriction.It is free of licensing restriction which are generally imposed by most commercial products.Open sourcing encourages open development , auditing process and also encourages participation of large number of people.



  • Classes:

A BioPHP class is a collection of various functions for manipulating biological data.Here we can define various classes containing definitions of restriction enzyme,Sequences,Sequence parsing and other biocomputing maipulation.

  • Functions:

We can write short  functions for small computations like parsing a sequence,complement,sequence alignment so that these functions could be directly utilized for bigger programs.

External Links

See also

Retrieved from ""
Personal tools