Ensembl Web

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Ensembl Web
Erin Pleasance Canadas Michael Smith Genome
Sciences Centre, Vancouver
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Homepage at http//www.ensembl.org
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Species-specific homepage
Search
Browse by chromosome
Statistics of current release
Site map
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Site Map
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Getting help
Click Back to homepage
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Text search
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GeneView
ContigView of gene
ContigView of gene and surrounding region
ProteinView
ExonView
TransView of transcript
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GeneView
(On the same page)
GeneView of homologues
References provided by SWISSPROT via GeneDAS
ExportView
GeneSNPView
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GeneView
(On the same page) Information provided for each
transcript individually
Links to external databases
AlignView of gene against external sequence
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GeneView
GOView Gene Ontology classification of function
DomainView of functional domains
FamilyView of other proteins in same family
TransView
ProteinView
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TransView
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ExonView
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GeneView
Click Back to
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ProteinView
Links to external databases
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GeneView
Click Back to
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ContigView
Chromosome and bands
Sequence contigs
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ContigView
Detailed View
Navigation
Position on chromosome
Gene annotations
Homologous sequences link to external databases
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ContigView
Basepair View
Forward strand
Reverse strand

• DNA sequence
• 6-frame translation
• Enzyme sites

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ContigView
Single nucleotide polymorphisms
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SNPView
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ContigView
Click Back to
Markers
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MarkerView
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ContigView
Click Back to
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ContigView
Forward strand
of surrounding region
caspase-3
Nearby genes
Reverse strand
Unstranded
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ContigView
Feature tracks
Explore all the menu options available!
Informs that other tracks are available
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ContigView
Feature tracks
Repeats appear in new track
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Exporting
From ContigView
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ExportView

• Flatfile (EMBL or GenBank) with features
• FASTA sequence only
• Feature list in a table
• Image of region

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ExportView
Flatfile
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ExportView
Click Back to
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EnsMart Data Mining
EnsMart is a powerful data mining toolset for
retrieving customised data sets from annotated
genomes, using criteria from Ensembl and third
party databases.

• To export
• Genes
• SNPs

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MartView Start
Indicates current query progress
Refine query
Reviews current query, indicates number of
objects to be retrieved
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MartView Filter
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186139601
186339601
Upload gene lists
Specify query requirements
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MartView Output
Can also output sequence, SNP info, gene structure
Output
Note number of entries to be retrieved
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MartView Results
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Similarity searching
BLAST for distantly related or protein
sequences slow SSAHA for nearly identical
sequences fast
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Similarity searching SSAHA
Copy-and-paste sequence OR upload file
(my_sequence.txt)
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Similarity searching SSAHA
Similar sequences on chromosomes
List of results
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Similarity searching SSAHA
Results shown in ContigView
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Other access methods AnchorView
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Other access methods Disease View
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Other access methods KaryoView
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Exercises

• Single nucleotide variations in the gene HFE have
  been associated with the disease hemochromatosis.
• What types of annotations represent this gene
  (eg. Ensembl novel gene, etc.)? How many Ensembl
  transcripts are annotated for this gene?
• How many coding SNPs are in the transcript for
  the longest protein product of this gene?
• What is the mouse homologue of this gene? Obtain
  a GenBank-format file of this homologue.
• How many EST transcripts appear to be equivalent
  to this gene? What markers overlap this gene?
  What is one type or repeat found in the 3 UTR of
  this gene?