Genome Browsers

Ensembl (EBI, UK) and UCSC (Santa Cruz, California)

http://www.ensembl.org/

http://genome.ucsc.edu/

Genome Browsers

UCSC

Ensembl

http://www.ensembl.org/

http://genome.ucsc.edu/

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

UCSCEnsembl

http://www.ensembl.org/

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 browser one can examine genomic conservation

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 !!