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Unriddle genomic codes using BioJava

life science software development life science blogs

Since the completion of the Human-genome project, deciphering the massive data produced becomes the primary focus of the scientist community. To analyse this data, bioinformaticians are required to develop such softwares and tools that can meet with the level of these complex data. The scalable, cross-platform, robust java framework leg-up the researchers to develop BioJava toolkit.

BioJava is an open-source project written entirely in Java programming language and is build to facilitate rapid bioinformatics software development and analysis using Java. It consists of many modules for manipulating biological data. For example, the core module of BioJava provides an API to perform basic operations with biological sequences, reading and writing of popular sequence file formats, translate DNA sequences into protein sequences, protein structure modules-to maintain local installations of PDB, load structures and manipulate them, perform standard analysis such as sequence and structure alignments, visualize structures, genome and sequencing modules-to create gene sequence objects from core module which allows parsing of popular file formats used in genomics, the alignment module provides an API that contains implementations of dynamic programming algorithms for sequence alignment, reading and writing of popular alignment file formats, a single- or multi- threaded multiple sequence alignment algorithm, protein disorder module for predicting disordered regions of proteins,  ModFinder module provides new methods to identify and classify protein modifications in protein 3D structures and amino acid properties module– to provide a range of accurate physicochemical properties for proteins.

When handling large data sets, BioJava outperforms all other already existing Bio-languages like BioPython, Bioperl etc. by its quick execution time and effective memory management and thus can be applied on whole genomic data.

Earlier were the days of wet-lab based researches and discoveries in genetics, but with the advancement in the information technology, era of bioinformatics now comes in play where most of the studies are first made in silicon. The escalating field of bioinformatics will provide exciting career opportunities to Java developers and opens a new business platform for biotech and pharmaceutical companies providing life science solutions using BioJava APIs.


1). Holland, Richard CG, Thomas A. Down, Matthew Pocock, Andreas Prlić, David Huen, Keith James, Sylvain Foisy et al. “BioJava: an open-source framework for bioinformatics.” Bioinformatics 24, no. 18 (2008): 2096-2097.

2). Prlić, Andreas, Andrew Yates, Spencer E. Bliven, Peter W. Rose, Julius Jacobsen, Peter V. Troshin, Mark Chapman et al. “BioJava: an open-source framework for bioinformatics in 2012.” Bioinformatics 28, no. 20 (2012): 2693-2695.

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