Using the Ensembl Genome Server to Browse Genomic Sequence Data

Xosé M. Fernández‐Suárez1, Michael K. Schuster1

1 EMBL‐European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom
Publication Name:  Current Protocols in Bioinformatics
Unit Number:  Unit 1.15
DOI:  10.1002/0471250953.bi0115s30
Online Posting Date:  June, 2010
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Abstract

The Ensembl project provides a comprehensive source of automatic annotation of the human genome sequence, as well as other species of biomedical interest, with confirmed gene predictions that have been integrated with external data sources. This unit describes how to use the Ensembl genome browser (http://www.ensembl.org/), the public interface of the project. It describes how to find a gene or protein of interest, how to get additional information and external links, and how to use the comparative genomic data. Curr. Protoc. Bioinform. 30:1.15.1‐1.15.48. © 2010 by John Wiley & Sons, Inc.

Keywords: computer graphics; databases; genetic; genetic variation; genomics; sequence homology; genome; genome sequence

     
 
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Table of Contents

  • Introduction
  • Basic Protocol 1: Search by Text/Keyword/Gene Name
  • Basic Protocol 2: Examining a Gene
  • Basic Protocol 3: Examining a Genomic Location
  • Support Protocol 1: Comparative Genomics: Gene Trees, Orthologues, and Paralogues
  • Support Protocol 2: Comparative Genomics: Pairwise Whole Genome Alignments
  • Support Protocol 3: Comparative Genomics: Multiple Whole Genome Alignments
  • Guidelines for Understanding Results
  • Commentary
  • Literature Cited
  • Figures
     
 
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Materials

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Figures

Videos

Literature Cited

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Internet Resources
   http://www.ensembl.org/
  Ensembl project home page
   http://www.biomart.org/
  BioMart Project
   http://vega.sanger.ac.uk/
  Vertebrate Genome Annotation (VEGA) at Sanger Institute
   http://www.ebi.ac.uk/interpro/
  InterPro
   http://www.genenames.org/
  HUGO Gene Nomenclature Committee (HGNC)
   http://www.geneontology.org/
  Gene Ontology Consortium
   http://biodas.org/
  Distributed Annotation System (DAS) and BioDAS
   http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=unists
  UniSTS
   http://www.sanger.ac.uk/Software/analysis/eponine
  Eponine
   http://emboss.sourceforge.net/
  The cpgreport program written by Gos Micklem is available on this site.
   http://www.repeatmasker.org/
  RepeatMasker program
   http://www.treefam.org/
  TreeFam
   http://phylomedb.bioinfo.cipf.es/
  PhylomeDB
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