Genome Browsers

Ensembl (EBI, UK) and UCSC (Santa Cruz, California) http://www.ensembl.org/ http://genome.ucsc.edu/

UCSC

Genome Browsers

http://genome.ucsc.edu/

Ensembl

http://www.ensembl.org/

Two main views (both browsers) •

Genomic region:

– Which genes located nearby – Evolutionarily conserved genomic elements – Regulatory elements •

Gene information:

– Gene description – Transcript information – Protein information – Homologs

Single Nucleotide Polymorphisms (SNPs) • Sequence variations within a species • Similar to mutations, but are simultaneously present in the population, and generally have little effect • Are being used as genetic markers (a genetic disease is e.g. associated with a SNP) • The Ensembl browser offers a nice SNP view

Alternative Transcripts Source: Wikipedia (http://www.wikipedia.org/)

Genome Browsers

http://www.ensembl.org/

Ensembl UCSC

http://genome.ucsc.edu/

UCSC Genome Browser

Choose a species, an assembly and a gene

Gene search results

Genomic Region

Genomic Datatypes (Tracks)

Genomic Region → Gene Record

Gene Record

Genomic Sequence Conservation

• Not only protein coding parts are conserved in evolution • Conserved non-coding genomic sequences can be involved in gene regulation (enhancers, silencers, insulators) • With the UCSC conservation browser one can examine genomic

Genomic Conservation (UCSC)

Copy Number Variation • People do not only vary at the nucleotide level (SNPs); short pieces genome can be present in varying number of copies (Copy Number Polymorphisms (CNPs) or Copy Number Variants (CNVs) • When there are genes in the CNV areas, this can lead to variations in the number of gene copies between individuals • With the UCSC browser CNVs can be examined

Copy Number Variation (UCSC)

UCSC vs Ensembl : Which is better ?

• They contain more or less the same information, but have different emphases • UCSC – is primarily focused on genomic regions – is easier to use • Ensembl – is primarily focused on genes – gives more detailed information and more flexible data export • Use whatever your are familiar with !!