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Transcript
Tutorial 12 Genome browser Genome browser • Free, open source, online browser for genomes. • Contains ~100 genomes, from nematodes to human. • Many tools that can be used to analyze genomic data. Genome browser http://genome.ucsc.edu/ How to find a gene of interest? genome Genome assembly location OR Gene name Lets take a look at the gene Information about the gene Sequences +Links to other databases Expression data Structural information RNA secondary structure Basic tracks RefSeq id Other names Summary on the gene Genomic position Gene length Sequences mRNA length Protein sequence, mRNA sequence Conservation Zoom in to compare base level Zooming in can help us identifying alternative splicing events Additional tracks Literature track RNA-Seq and regulation Common SNPs Tables How to download a gene sequence? Clade, genome, assembly Group and track “Known genes” table position Choose “sequence” Different parts of the gene Other possible tracks from the table browser miRNAs in the human genome Adding custom tracks browser position chr17:41243452-41277500 track name=unknown description="unknown genomic element" color=255,0,0, chr17 41244000 41246000 Here’s our custom track! http://genome.ucsc.edu/goldenPath/help/hgTracksHelp.html#CustomTracks BLAT BLAT • BLAT on DNA is designed to quickly find sequences of 95% and greater similarity of length 25 bases or more. • BLAT is not BLAST. DNA BLAT works by keeping an index of the entire genome in memory. The index consists of all overlapping 11-mers stepping by 5. • Protein BLAT works in a similar manner : : Examples 1. In which chromosome can you find the CFTR gene in human? 2. In which chromosome can you find the CFTR gene in mouse? 3. How many exons does the CFTR gene have? 4. Which genes are close to CFTR on chromosome 7? Zooming out 5. What is the orientation of the gene? Plus or minus? 6. download the promoter area of the CFTR gene (1000 bp)
