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
UCSC display
but release timing is different between sites
Why use Ensembl

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
Over 50 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.
CDS definition
mix of experimental and computationally derived sources

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
A new genebuild for a species is only done if there is a new genome assembly or lots of new supporting evidence

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
ENSMUST
ENSMUSP
ENSMUSG

11. Ensembl Organization Views designed into four classes Gene Transcript
Location (Genome Browser)
Variation
Not covering
What’s the conservation track?
How do I zoom in and change the gene focus.
Un-stacking a track (e.g. human cDNAs)
Adding a track (i.e. variations)

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
Ensembl 2009 Nucleic Acids Research
PMID:
Bert Overduin, Ph.D. Ensembl