A tutorial for the genomics module of BioJava
|
The genome module of BioJava provides an API that allows to
|
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
The content of this tutorial is available under the CC-BY license, available here.
BioJava 5: A community driven open-source bioinformatics library
Aleix Lafita, Spencer Bliven, Andreas Prlić, Dmytro Guzenko, Peter W. Rose, Anthony Bradley, Paolo Pavan, Douglas Myers-Turnbull, Yana Valasatava, Michael Heuer, Matt Larson, Stephen K. Burley, & Jose M. Duarte
PLOS Computational Biology (2019) 15 (2):e1006791.
Navigation: Home | Book 4: The Genomics Module