report on Bioperl
Bioperl is a collection of Perl modules that facilitate the development of Perl scripts for bioinformatics applications. As such, it does not include ready to use programs. In order to take advantage of bioperl, the user needs a basic understanding of the Perl programming language including an understanding of how to use Perl references, modules, objects and methods. Bioperl is open source software that is still under active development. It ability to freely examine and modify source code and exemption from software licensing fees. Any user can test bioperl using minimum installation and find out that it is useful to him or not that how he or she don’t have to complete install the program.
Bioperl uses three types of bioperl objects
1. Sequence object :Most common operation perform by Esq. Object like general string manipulation in DNA.Most common sequence manipulations can be performed with Seq. These capabilities are described in the Bio::Seq manage.
2. Location object :A Location object is designed to be associated with a Sequence Feature object in order to show where the feature is on a longer sequence. Location objects can also be standalone objects used to describe positions. The reason why these simple concepts have evolved into a collection of rather complicated objects is that:
a) Some objects have multiple locations or sub-locations (e.g. a gene's exons may have multiple start and stop locations) b
) In unfinished genomes, the precise locations of features are not known with certainty.
The documentation of the various modules in the Bio::Locations directory
3.Interface object and implementation object: One goal of the design of Bioperl is to separate interface and implementation objects. An interface is solely the definition of what methods one can call on an object, without any knowledge of how it is implemented. An implementation is an actual, working implementation of an object. In bioperl, the interface objects usually have names
Bioperl uses three types of bioperl objects
1. Sequence object :Most common operation perform by Esq. Object like general string manipulation in DNA.Most common sequence manipulations can be performed with Seq. These capabilities are described in the Bio::Seq manage.
2. Location object :A Location object is designed to be associated with a Sequence Feature object in order to show where the feature is on a longer sequence. Location objects can also be standalone objects used to describe positions. The reason why these simple concepts have evolved into a collection of rather complicated objects is that:
a) Some objects have multiple locations or sub-locations (e.g. a gene's exons may have multiple start and stop locations) b
) In unfinished genomes, the precise locations of features are not known with certainty.
The documentation of the various modules in the Bio::Locations directory
3.Interface object and implementation object: One goal of the design of Bioperl is to separate interface and implementation objects. An interface is solely the definition of what methods one can call on an object, without any knowledge of how it is implemented. An implementation is an actual, working implementation of an object. In bioperl, the interface objects usually have names