How to access genomic information

using Ensembl

August 2005

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GOAL

Status of the human sequencefinished red /orange~96% (99.999% accurate)

30-40% repetitive elements (eg Alpha satellite, Alu repeats)

All known genes, correctly identified (99.74%)

heterochromatin~4% grey

Assembled draft sequence totals 2.85 Gb

4 of 42Finishing the euchromatic sequence of the human genome, Nature 431:931-45 (2004)

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Analysis DB

CPU

Final DB

SupportingDatabases

SNP

ManualAnnotation

Ensembl

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Genome browsingwhy present the whole genome?

• Explore what is in a chromosome region• See features in and around a specific gene• Search & retrieve across the whole genome• Investigate genome organization• Compare to other genomes

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Genome browsers

• NCBI Map Viewer

• UCSC Human Genome Browser

• Ensembl – public site + installable system

http://www.ensembl.org

http://www.ncbi.nlm.nih.gov/mapview

http://genome.ucsc.edu

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Introduction to the

Ensembl web site Ensembl … …

takes genomic sequence assemblieshuman build 35, mouse, rat, mosquito…

adds annotation and links automated process

presents all the data on a web site

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Basic Genome Annotation

• Genes– Genomic location– Gene model structures

• Exons• Introns• UTRs

– Transcript(s)

• Pseudogenes• Non-coding RNA

– Protein(s)– Links to other sources of information

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Advanced Genome Annotation

• Cytogenetic bands• Polymorphic markers

– Sequence Tagged Sites (STS)

• Genetic variation– Single Nucleotide Polymorphisms (SNPs)

– Deletion-Insertion Polymorphisms (DIPs)

– Short Tandem Repeats (STRs)

• Repetitive sequences• Expressed Sequence Tags (ESTs)• cDNAs or mRNAs from related species• Regions of sequence homology

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How to get started … …

• Species homepage

• Map View

• Text search

• BLAST

• SSAHA

Homepage

MapView

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BLAST and SSAHA

See blast hit on genome

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http://genome.imim.es/~nlopez/UVIC/seq.fas

Query sequence:

In which chromosome you get the best hit?Explore the alignment of the query sequence with the genomeIs this is a sequence of a gene?If so, which one?Explore the region around this sequence

Practical:

BLAST and SSAHA practical

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Regions, maps and markers

MarkerView

SNPView

GeneSNPView

ContigView

CytoView

SyntenyView

MultiContigView

EnsemblContigView

ContigView close-up

Transcriptsred & black(Ensembl predictions)Blue (Vega)

Pop-up menu

ContigView - Chromosome 20 close-up

Manualannotationvia Vega

Ensembl predictions

Ensembl EST-based predictions

Chromosomes with manual annotation (http://vega.sanger.ac.uk): 1, 6, 7, 9, 10, 13, 14, 16, 18, 19, 20, 22, X and Y

CytoView

GeneSNPView

SNPView

MarkerView

SyntenyView

MultiContigView

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Genes & gene products

GeneView

TransViewExonView

ProteinView

FamilyView

DomainView

GOView

DiseaseView

EnsemblGeneView

ExonViewTransView

ProteinView

FamilyView

GOView

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Ensembl practical

Type the name of your favorite gene (i.e. BRCA2) and explore all the sections of ensembl for this gene.

•Has this gene an ortholog in mouse?•How many different transcript do we know of this gene?•How many exons has the longest transcript?•Which functional annotations has this gene? (hint: check at GO annotations•Can you find SNPs in this gene?