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Genome Browsers

Genome Browsers. Ensembl (EBI, UK) and UCSC (Santa Cruz, California). http://www.ensembl.org/. http://genome.ucsc.edu/. Genome Browsers. UCSC. Ensembl. http://genome.ucsc.edu/. http://www.ensembl.org/. Two main views (both browsers). Genomic region: Which genes located nearby

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Genome Browsers

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

  2. Genome Browsers UCSC Ensembl http://genome.ucsc.edu/ http://www.ensembl.org/

  3. 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

  4. 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

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

  6. Genome Browsers UCSC Ensembl http://www.ensembl.org/ http://genome.ucsc.edu/

  7. UCSC Genome Browser

  8. Choose a species, an assembly and a gene

  9. Gene search results

  10. Genomic Region

  11. Genomic Datatypes (Tracks)

  12. Genomic Region → Gene Record

  13. Gene Record

  14. 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

  15. Genomic Conservation (UCSC)

  16. 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

  17. Copy Number Variation (UCSC)

  18. 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 !!

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