The Ensembl Database

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The Ensembl Database
Erin Pleasance Steven Jones Canadas Michael
Smith Genome Sciences Centre, Vancouver
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www.ensembl.org
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What is Ensembl?

• Public annotation of mammalian and other genomes
• Open source software
• Relational database system
• The future of genomic bioinformatics?

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The Ensembl Project
Ensembl is a joint project between EMBL European
Bioinformatics Institute and the Sanger
Institute to develop a software system which
produces and maintains automatic annotation on
eukaryotic genomes. Ensembl is primarily funded
by the Wellcome Trust
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The Ensembl Project
The main aim of this campaign is to encourage
scientists across the world - in academia,
pharmaceutical companies, and the biotechnology
and computer industries - to use this free
information.
- Dr. Mike Dexter, Director of the Wellcome Trust
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Goal An Accessible, Annotated Genome
Diagram of contigview as what we want in the end
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Ensembl Software System

• Uses extensively BioPerl (www.bioperl.org)
• The free mySQL database
• Entire Ensembl code base is freely available
  under Apache open source license.
• Mainly written in Perl, extensions in C. Some
  viewers have been written in Java (e.g. Apollo).

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Ensembl Genome Annotation

• Utilizes raw DNA sequence data from public
  sources
• Creates a tracking database (The Ensembl
  database)
• Joins the sequences - based on a sequence
  scaffold or Golden Path
• Automatically finds genes and other features of
  the sequence
• Associates sequence and features with data from
  other sources
• Provides a publicly accessible web based
  interface to the database

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The Genome Problem

• The problem with the genome (particularly human)
  is that it is large, complicated, and opaque to
  analysis (Ewan Birney, Ensembl)
• Genome features to identify include
• Genes protein coding, RNA, pseudogenes
• Regulatory elements
• SNPs, repeats, etc.

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DNA sequence in Ensembl

• Sequences are determined in fragments (contigs)
• Features cross boundaries between fragments
• Entire sequence too large and changes too much
  (constantly updated and reassembled) to be stored
  as one long database entry

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DNA sequence in Ensembl

• Core design feature is the virtual contig
  object
• Allows genome sequence to be accessed as a single
  large contiguous sequence even though it is
  stored as a collection of fragments
• VC object handles reading and writing features to
  the DNA sequence

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Ensembl Gene Build System

• Three-part gene build system
• Best in genome matches for known genes
• Alignment of homologous genes
• Ab initio gene finding
• Genes predicted on repeat-masked DNA
• All genes predicted based on experimental
  (available sequence) evidence

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Best in genome predictions

• Find known proteins from SPTREMBL on genome using
  pmatch
• Incorporate cDNAs using exonerate and EST_genome
• Align with gaps placed preferentially at splice
  consensus sites
• Allows prediction of 5 and 3 UTRs
• Refine predictions using genewise

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Best in genome predictions

• Alignments shown in ContigView

UTRs predicted
Known gene (p53)
ContigView of best in genome gene with associated
evidence
Proteins aligned
Unigene clusters aligned
cDNAs aligned
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Homology predictions

• Align homologous proteins using BLAST, genewise
• Paralogs (from same organism)
• Orthologs (from closely related organisms)
• Assemble novel genes

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Ab initio gene predictions

• Use Genscan to identify novel exons
• Confirm exons by BLAST to known proteins, mRNAs,
  UniGene clusters
• Based on ab initio predictions but require
  homology evidence

ContigView of homology gene with associated
evidence
Unigene clusters aligned
Proteins aligned
Novel gene
GenScan predictions
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Pseudogenes

• Many pseudogenes also predicted

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Ensembl Gene Build System

• Resulting Ensembl genes are highly accurate
  with low false positive rates
• Ensembl human gene identifiers are 95 stable
  between builds

Snapshot or stats on genes
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Ensembl EST genes

• ESTs not accurate enough to produce Ensembl
  genes, but important especially for identifying
  alternative transcripts
• Create an independent set of EST genes

Known gene
EST genes
Unigene clusters aligned
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Ensembl EST genes

• Map ESTs to genome using Exonerate, BLAST, and
  EST2Genome
• Define transcripts by merging redundant ends,
  setting splice sites to common ends
• Finds splice sites and defines UTRs
• Alternative transcript predicted if at least one
  alternatively spliced EST exists
• Process transcripts with Genomewise to find
  longest ORF for each

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Ensembl EST genes

• Evidence for genes shown (ExonView)

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Manual gene annotation Otter

• Manual annotation done with applications eg.
  Apollo
• Otter database/server allows manual annotations
  to be integrated with automated annotations

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Manually curated genes VEGA

• Chromosomes 6,7,13,14, 20 and 22 contain manually
  curated genes from VEGA database

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Gene information in Ensembl GeneView
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Transcript information in Ensembl TransView
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Protein information in Ensembl ProteinView
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Comparative genomics in Ensembl

• Gene orthologue pairs
• Human lt-gt Mouse lt-gt Rat lt-gt Fugu lt-gt Zebrafish
• C. elegans lt-gt C. briggsae
• Fly lt-gt Mosquito
• DNA homology
• Human lt-gt Mouse lt-gt Rat

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Comparative genomics in Ensembl Gene orthologs

• Gene ortholog pairs shown in GeneView
• Calculated by BLAST (reciprocal best BLAST hits,
  or BLAST synteny)
• dN/dS nonsynonymous/synonymous change (measure
  of selection)

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Comparative genomics in Ensembl DNA homology

• DNA homology shown in ContigView

Mouse and rat homology
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Comparative genomics in Ensembl Synteny

• Large-scale homology shown in SyntenyView
• Synteny homologous sequence blocks, in same
  order and orientation

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Other features in Ensembl

• Menus provide other feature options
• Features eg. SNPs and markers have special views

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Other data sources in Ensembl

• Ensembl incorporates gene and feature info from
  many other datasources

OMIM
SwissProt
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Other data sources in Ensembl Link out
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The Distributed Annotation System

• Allows viewing third-party annotation of the
  genomic scaffold
• Users can choose the annotation they are
  interested in
• Features are viewed in consistent user
  interface/display
• Allows specialized feature annotation and the
  comparison of different methodologies

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DAS Selecting data
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GeneDAS

• GeneDAS allows exchange of annotations on gene
  level
• eg. access to SwissProt annotations from GeneView

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DAS Add your own annotations

• Anyone can add data and upload it to DAS server
  for others to view

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Sequence similarity searching

• Two search methods
• SSAHA very fast, good for identifying near-exact
  DNA-DNA matches
• BLAST slower but more accurate, can do DNA or
  protein searches
• Can search against any species
• Can search against genomic sequence, cDNAs
  (Ensembl or Genscan), or protein sequences

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(No Transcript)
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Hits relative to genome
Show alignment A, sequence S, or ContigView
C
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BLAST results
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Data Mining with EnsMart

• EnsMart - organizes data from Ensembl into a
  query-optimized database
• Allows very fast, cross-data source querying
• Accessible from
• Ensembl website (MartView)
• Stand-alone application (MartExplorer)
• Command-line interface (MartShell)
• Extremely powerful for data mining

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Dataming with Ensmart
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• Choose focus gene set or SNPS
• Choose organism (any species in Ensembl)

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• Filter genes based on info about
• Region
• Genes
• Diseases
• Expression patterns
• Multi-species comparisons
• Protein domains and families
• SNPs

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• Choose output type
• Features (genes with associated info)
• SNPs
• Structures (of genes eg. exons)
• Sequences
• Choose what information to output

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Multiple Programming Interfaces now exist for
Ensembl
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Another example of how to utilize the Ensembl
database Sockeye
www.bcgsc.ca/bioinfo/software
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Apollo java viewer
www.ensembl.org/apollo
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Ensembl updates

• Monthly
• Include
• Changes in genome builds (with new annotations)
• Changes in code or database schema
• Additional views and tools on website

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Pre-Ensembl

• Full annotation can take weeks
• Pre-Ensembl site provides in-progress annotation
• Placement of known proteins
• Ab initio gene predictions
• Repeat masking
• BLAST and SSAHA searching

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Ensembl Software System

• Software can be accessed by FTP
• Can also be accessed through CVS (concurrent
  versions system)
• Possible to set up a mirror of the entire Ensembl
  system.

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Further Information

• The Ensembl Project www.ensembl.org
• VEGA vega.sanger.ac.uk
• EnsMart www.ensembl.org/EnsMart/
• Distribributed Annotation System www.biodas.org
• Human Genome Central Resources
  www.ensembl.org/genome/central
• References
• Ensembl
• Hubbard et al, 2002. NAR 30 (1), 38-41.
• Clamp et al, 2003. NAR 31 (1), 38-42.
• Birney et al, 2004. NAR 32, D468-D470.
• EnsMart Birney et al, 2004. Genome Res. 14,
  160-169.