Open-Source Software for Large-Scale Genome Analysis
  • Anne ParkerEmail author
  • Fiona Cunningham


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.


Gene Prediction Analysis Annotation Perl Web Interface Display 

Suggested Reading


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

Ensembl: An Open-Source Tool

  1. 2.
    Raymond, E.S. (1999) The Cathedral and the Bazaar.Google Scholar

The Ensembl Code Base

  1. 3.
    Conway, D., (2000) Object-Oriented Perl: A Comprehensive Guide to Concepts and Programming Techniques.Google Scholar
  2. 4.
    Havana (Human and Vertebrate Analysis and Annotation):

Using the Ensembl Website

  1. 5.
    Blast (Basic Local Alignment and Search Tool):
  2. 6.
  3. 7.
    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.Google Scholar
  4. 8.

Using the Ensembl API

  1. 9.

Copyright information

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

Authors and Affiliations

  1. 1.Wellcome Trust Sanger InstituteCambridgeUK
  2. 2.Wellcome Trust Sanger InstituteCambridgeUK

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