http:www.ensembl.orgindex.html

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http//www.ensembl.org/index.html
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ENSEMBL

• Ensembl is a joint project between EMBL - EBI and
  the Sanger Institute to develop a software system
  which produces and maintains automatic annotation
  on selected eukaryotic genomes. Ensembl is
  primarily funded by the Wellcome Trust.
• This site provides free access to all the data
  and software from the Ensembl project. Click on a
  species name to browse the data.

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• What's New in Ensembl 42 (December 2006)
• New - User accounts (all species)
• BioMart Release 0.5 (all species)
• New species - Duck-billed Platypus
• New Dog assembly and genebuild
• New Chicken assembly and genebuild
• Affy mappings for Chimp
• Compara DNA/DNA alignments (all species)

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• Use Ensembl to...
• Run a BLAST search (by species)
• Search Ensembl
• Align sequences
• Data mining BioMart
• Export data
• Much more

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Ensembl Data Displays List
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• Docs and downloads
• Data
• Downloads
• FASTA Database Files
• FTP Directory Structure
• Searching
• Comparative Genomics
• Genome Annotation
• Custom Annotation
• Ensembl HelpDesk
• Ensembl Courses

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• Other Ensembl websites
• archive! - past releases of Ensembl
• VEGA - Vertebrate Genome Annotation
• EBI Genome Reviews database - mainly archaea and
  bacteria.
• Trace server

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• Mammalian genomes
• Homo sapiens NCBI 36 Vega (Human)
• Pan troglodytes PanTro 2.1 (Chimp)
• Macaca mulatta MMUL 1.0 (Monkey)
• Mus musculus NCBI m36 Vega (Mouse)
• Rattus norvegicus RGSC 3.4 (Rat)
• Bos taurus Btau 2.0 (Cow)
• Sus scrofa clone map (Pig)
• Canis familiaris CanFam 2.0 UPDATED! (Dog)
• Felis catus (Cat)
• Loxodonta africana BROAD E1 (Elephant)
• Oryctolagus cuniculus (Rabbit)
• Echinops telfairi TENREC (Hedgehog)
• Dasypus novemcinctus (Armadillo)
• Myotis lucifugus (Bat)
• Monodelphis domestica MonDom 4.0 (Opossum)
• Ornithorhynchus anatinus Oana-5.0 NEW! (Platypus)
• Cavia porcellus cavPor1 (Guinea Pig)

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• Other species
• Aedes aegypti AaegL1 (Mosquito Yellow Fever)
• Anopheles gambiae AgamP3 (Mosquito Malaria)
• Caenorhabditis elegans WS160 (Worm)
• Ciona intestinalis JGI 2 (Sea Squirt)
• Ciona savignyi CSAV 2.0 (Sea Squirt)
• Danio rerio Zv6 Vega (Zebrafish)
• Drosophila melanogaster BDGP 4.3 (Fly)
• Gallus gallus WASHUC2 UPDATED! (Chicken)
• Gasterosteus aculeatus BROAD S1 (Stickleback
  Fish)
• Oryzias latipes HdrR (Medaka Fish)
• Saccharomyces cerevisiae SGD1.01 UPDATED! (Yeast)
• Takifugu rubripes FUGU 4.0 (Fugu Fish)
• Tetraodon nigroviridis TETRAODON 7 (Puffer Fish)
• Xenopus tropicalis JGI 4.1 (Frog)

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• Powered by Ensembl
• Glovar shows sequence variation in a genomic
  context
• DeCIFR legume project Automated annotation and
  display of legume genomes
• AtEnsembl Arabidopsis thaliana genome browser
• Gramene A Comparative Mapping Resource for Grains
• CADRE Central Aspergillus Data Repository
• Sigenae EST ContigBrowser
• COSMIC (Catalogue of Somatic Mutations in Cancer)
  somatic sequence variant
• MVP (Methylation Variable Positions) Human
  Epigenome Project.
• S. pombe Gene Expression Viewer under various
  environmental conditions.
• PupaSuite optimal sets of SNP for genotyping
• ISACGH chromosomal copy number alterations
• Phylopat presence or absence of genes or proteins
  in eukaryote species

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• http//atensembl.arabidopsis.info/index.html
• Arabidopsis Ensembl is a genome browser for the
  commonly studied plant model organism Arabidopsis
  thaliana.

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• Ensembl text search
• Enter the string you wish to search for in the
  box above.

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Ensemble Human Contig View
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Features
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Comparative
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DAS Sources
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Human Dasconf View
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DAS Wizard Step 1 of 3 Data location
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KEGG DAS
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DAS Wizard Step 2 of 3 Data appearance
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DAS Wizard Step 3 of 3 Display configuration
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Added DAS feature (Uniprot)
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Repeats

• All repeats
• Dust
• LTRs
• Low complexity regions
• Other repeats
• RNA repeats
• Satellite repeats
• Simple repeats
• Tandem repeats
• Type I Transposons/LINE
• Type I Transposons/SINE
• Type II Transposons
• Unknown

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Decorations
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Export

• Include PDF links
• Include SVG links
• Include POSTSCRIPT links
• Export data (tool)
• Export information about region
• Export sequence as FASTA
• Export EMBL file
• Export Gene info in region (BioMart)
• Export SNP info in region (BioMart)
• Export Vega info in region (BioMart)

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• Select region/feature to Export

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Configuring Flat File output

• \

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Contig Image size
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Ensemble Gene View
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Genomic sequence
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GeneSeqAlign View
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GeneTree View
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JalView
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Export alignment
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Variation (SNP) View
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SNP Tables
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SNP Reports
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Transcript View
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Transcript View Key
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Feature View
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GO View
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GO - Family Report
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Exon Information
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Protein Information
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Chromosome view
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Karyotype View
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Synteny View
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Large Downloads
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Ensembl Blast
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http//www.unc.edu/dcfargo/Ensembl_class/

• BLA_OBQCIfjjA
• http//www.ensembl.org/Homo_sapiens/blastview/BLA_
  OBQCIfjjA

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Results are retained for 7 days
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Configuration and Results
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Blast results

• Alignment Summary
• A S G C 1888 2627 Chr4 25399306
  25400049 - 525 1.5e-281 85.48 744
• A S G C 1002 1262 - No data 213
  1.1e-51 90.80 261
• A S G C 2731 3058 - Chr4 25383463
  25383784 200 2.9e-47 81.68 333
• A S G C 389 621 No data 192 1.6e-45
  91.14 237
• A S G C 1523 1717 Chr4 25431661
  25431855 - 171 1.5e-281 93.85 195
• Alignment, Sequence, Genomic, Chromosome

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Data Mining BioMart
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Data Set Count
 Dataset 31,148 / 31,148 Genes
Attributes (Features)
Filters
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 Attributes (Features)
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Filters
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BioMart Results
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Attributes (Sequences)