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Ensembl

Ensembl. Genome Repository. Main Data Repositories. Ensembl- BLAST or BLAT UCSC - BLAT NCBI (Entrez) - BLAST Ensembl, NCBI, and UCSC use the same human genome assembly that is generated by NCBI. Ensembl. Provide automatic annotation of sequenced genomes Integrate with biological data

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Ensembl

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  1. Ensembl Genome Repository

  2. Main Data Repositories • Ensembl- BLAST or BLAT • UCSC - BLAT • NCBI (Entrez) - BLAST • Ensembl, NCBI, and UCSC use the same human genome assembly that is generated by NCBI

  3. Ensembl • Provide automatic annotation of sequenced genomes • Integrate with biological data • Make available from web • Genome Browser • Web interface • BioMart • Direct database access Perl API

  4. Outline • Where the data comes from • Questions that can be answered

  5. Ensembl Genomes

  6. Genome Annotation • Identify elements on the genome • Attach biological information to the elements • Automatic annotation and curation Vega/Havana

  7. Annotation • Addition of positional, functional, regulatory and evolutionary datasets to a raw assembled genome. • Genes, exon-intron boundaries, protein products, miRNAs, alternative splicing, transcriptional start sites, expression,orthologs, paralogs, repeats, structural features, syntenic relationships, ChIP-chip data ... • Based on experimental data and computational predictions.

  8. Genebuild • Align species-specific proteins to the genome to create CDS models (targeted build) • Align proteins from closely related species to locate additional CDS models (similarity build) • Add UTRs using cDNA/EST evidence and ditag data • Cluster transcripts into genes • Classify transcripts • Name genes

  9. Human/Mouse Genebuild • additional steps not included in the standard Ensembl build. • For both species, transcripts from the Consensus Coding Sequence (CCDS) set are imported directly and not altered by the genebuild process. • In addition, where manual curation is available for a transcript, the Ensembl and HAVANA transcript models are compared. • The Ensembl and HAVANA models are merged when they agree on the same coding sequence

  10. Ensembl Identifiers • ENS_Species_Type_00000_ID • Species: blank for human for all other species a three letter code (MUS - mouse) • Type: G (gene), T (transcript), P (protein) • ID: six-digit number • ENSMUST00000118022 • ENSMUSP00000113891 • ENSMUSG00000021944

  11. Ensembl Organization • Views designed into four classes • Gene • Transcript • Location (Genome Browser) • Variation

  12. Questions • Are there splice variants? • How do I find orthologs and paralogs? • Are there variations in the genomic sequence? • How can I download different parts of the mRNA sequence? • What protein domains exist? • Gene Ontology • Can I download sets of data (DNA, cDNA, protein) for a species? • BioMart question

  13. Resources • Ensembl Tutorials http://www.ensembl.org/info/website/tutorials/index.html • Ensembl 2009 Nucleic Acids Research PMID: 19033362 • Bert Overduin, Ph.D. Ensembl http://www.ebi.ac.uk/~bert/workshops/london_080509/browser_london_080509.pdf

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