Transcript Genoombrowsers - Radboud Universiteit

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:
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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 !!