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Ensembl

Open-Source Software for Large-Scale Genome Analysis

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Bioinformatics for Systems Biology

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Abstract

Ensembl is a Perl-based application designed for the easy retrieval and analysis of genomic data. Both a command-line API and a web interface are available, allowing the manipulation of sequences and associated genomic features. Additionally, the web interface displays this information in a variety of graphical formats. All software and associated data are freely downloadable and are released under an open-source licence.

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Suggested Reading

Introduction

  1. Hubbard, T.J.P. et al. (2007) Ensembl 2007, Nucleic Acids Res. 2007, Jan 1; Database Issue.

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Ensembl: An Open-Source Tool

  1. Raymond, E.S. (1999) The Cathedral and the Bazaar.

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The Ensembl Code Base

  1. Conway, D., (2000) Object-Oriented Perl: A Comprehensive Guide to Concepts and Programming Techniques.

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  2. Havana (Human and Vertebrate Analysis and Annotation): http://www.sanger.ac.uk/HGP/havana/

Using the Ensembl Website

  1. Blast (Basic Local Alignment and Search Tool): http://www.ncbi.nlm.nih.gov/BLAST/

  2. BioMart: http://www.biomart.org

  3. Fernandez, X.M. and Schuster, M. (2007) Using the Ensembl Genome Server to Browse Genomic Sequence Data, Current Protocols in Bioinformatics, Supplement 16, Unit 1.15.

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  4. BioDAS: http://www.biodas.org

Using the Ensembl API

  1. BioPerl: http://www.bioperl.org

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Author information

Authors and Affiliations

  1. Wellcome Trust Sanger Institute, Cambridge, UK

    Anne Parker

  2. Wellcome Trust Sanger Institute, Hinxton, Cambridge, UK

    Fiona Cunningham

Authors
  1. Anne Parker
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  2. Fiona Cunningham
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Corresponding author

Correspondence to Anne Parker .

Editor information

Editors and Affiliations

  1. Wayne State University, Detroit, MI, USA

    Stephen Krawetz

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© 2009 Humana Press, a part of Springer Science+Business Media, LLC

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Parker, A., Cunningham, F. (2009). Ensembl. In: Krawetz, S. (eds) Bioinformatics for Systems Biology. Humana Press. https://doi.org/10.1007/978-1-59745-440-7_24

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