Abhishek Tiwari:Bioinformatics Toolkits

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Bioinformatics Toolkits

Geneious http://www.geneious.com/

Geneious(Free for academic use) provides sophisticated genome & proteome research tools, protein or molecular visualization, publication literature search and storage tools and more, with revolutionary usability.Plugins extend Geneious's functionality by providing additional document importers or exporters, document viewers, database access or operations such as alignment or tree building. Anyone can write plugins using our freely available Public API – in fact, most of Geneious's standard functionality is internally provided by plugins.

BioPerl www.bioperl.org

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 the sense that many commercial packages and free web-based interfaces do (e.g. Entrez, SRS). On the other hand, Bioperl does provide reusable Perl modules that facilitate writing Perl scripts for sequence manipulation, accessing of databases using a range of data formats and execution and parsing of the results of various molecular biology programs including Blast, clustalw, TCoffee, genscan, ESTscan and HMMER. Consequently, bioperl enables developing scripts that can analyze large quantities of sequence data in ways that are typically difficult or impossible with web based systems.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.

BioJava http://biojava.org

BioJava is an open-source project dedicated to providing a Java framework for processing biological data. It include objects for manipulating biological sequences, file parsers, DAS client and server support, access to BioSQL and Ensembl databases, tools for making sequence analysis GUIs and powerful analysis and statistical routines including a dynamic programming toolkit.

BioJava is used in several real-world bioinformatics applications and has been used for bioinformatics analysis in a number of published studies. For example Biosense a commercial informatics offering from Inforsense that uses BioJava under the hood.

BioPython http://biopython.org/

The Biopython Project is an international association of developers of freely available Python tools for computational molecular biology.Project develop reusable Python code for anything related to biology and computing.Using BioPython one can do nearly all works which are possible using BioPerl and BioJava.

MathWorks http://www.mathworks.com/products/bioinfo/

MathWorks provides Bioinformatics Toolbox for extending MATLAB.The Bioinformatics Toolbox offers computational molecular biologists and other research scientists an open and extensible environment in which to explore ideas, prototype new algorithms, and build applications in drug research, genetic engineering, and other genomics and proteomics projects. The toolbox provides access to genomic and proteomic data formats, analysis techniques, and specialized visualizations for genomic and proteomic sequence and microarray analysis. Most functions are implemented in the open MATLAB language, enabling you to customize the algorithms or develop your own.

NCBI ToolBox http://www.ncbi.nlm.nih.gov/IEB/ToolBox/MainPage/index.html

The NCBI ToolBox model and code is used extensively within NCBI for the internal pipelines and tools such as GenBank, Entrez, BLAST, Sequin, OMIM, RefSeq, and others. These tools are supported in the sense that they are designed to work in many environments outside NCBI. The NCBI ToolBox consists of three major parts:

• Data Model - An explicit data model of biological sequences, structures, bibliographic data, and associated annotations.
• Data Encoding - A formal specification and encoding rules. The telecommunications standard, ASN.1, has been used for this. Recently it has been mapped to a similar language, XML.
• Programming Libraries - Originally written in a portable dialect of C. Recently a new generation is being written in C++.

Molecular Biology Toolkit (MBT) http://mbt.sdsc.edu/

The Molecular Biology Toolkit (MBT) is a Java-based protein visualization and analysis toolkit. The toolkit provides classes for efficiently loading, managing and manipulating protein structure and sequence data. The MBT also provides a rich set of graphical 3D and 2D visualization components which can be easily "plugged together" to produce applications having sophisticated graphical user interfaces. Yet, with all of the GUI components provided in the toolkit, the core data i/o and manipulation classes may be used to write completely non-graphical applications (say, for implementing pure analysis codes, or, for producing a non-graphical "back end" for web-based applications).