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://www.ensembl.org/ http://genome.ucsc.edu/

5. 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

8. 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

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

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

16. UCSC Genome Browser

17. Choose a species, an assembly and a gene

18. Gene search results

19. Genomic Region

20. Genomic Datatypes (Tracks)

21. Genomic Region → Gene Record

22. Gene Record

23. 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

24. Genomic Conservation (UCSC)

25. 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

26. Copy Number Variation (UCSC)

27. 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 !!