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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 – 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 Ensembl http://www.ensembl.org/ http://genome.ucsc.edu/ UCSC 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 !!