A tutorial for the genomics module of BioJava
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The genome module of BioJava provides an API that allows to
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This tutorial is split into several chapters.
Chapter 1 - Quick Installation
Chapter 2 - Reading gene names information from genenames.org
Chapter 3 - Reading chromosomal positions for genes. (UCSC's refFlat.txt.gz )
Chapter 4 - Reading GTF and GFF files
Chapter 5 - Reading and writing a Genebank file
Chapter 5 - Reading karyotype (cytoband) files
Chapter 6 - Reading genomic DNA sequences using UCSC's .2bit file format
BioJava: an open-source framework for bioinformatics in 2012
Andreas Prlic; Andrew Yates; Spencer E. Bliven; Peter W. Rose; Julius Jacobsen; Peter V. Troshin; Mark Chapman; Jianjiong Gao; Chuan Hock Koh; Sylvain Foisy; Richard Holland; Gediminas Rimsa; Michael L. Heuer; H. Brandstatter-Muller; Philip E. Bourne; Scooter Willis
Bioinformatics (2012) 28 (20): 2693-2695.
The content of this tutorial is available under the CC-BY license.
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