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URL: http://github.com/biojava/biojava-tutorial/tree/master/genomics

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README.md

The BioJava - Genomics Module

A tutorial for the genomics module of BioJava

About

The genome module of BioJava provides an API that allows to
  • Parse popular file formats used in genomcs
  • Convert from one file format to another
  • Translate DNA sequences into protein sequences

Index

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

License

The content of this tutorial is available under the CC-BY license, available here.

Please Cite

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.
doi pubmed

Navigation: Home | Book 4: The Genomics Module

Prev: Book 3: The Structure Modules
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