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This tutorial shows how to use the UCSC genome browser to find a list of genes in a given genomic region.

Transcript of video

0:54 - Set up the Genome Browser display to see the genes in your region.
1:31 - Zoom to a cytoband.
1:54 - Display only one isoform per gene.
2:20 - Use the table Browser to get the list of genes in your region.
3:40 - Use knownCanonical table in the table Browser to list only one isoform per gene.
 
run time: 4:33


This tutorial shows how to navigate between exons of a gene using the UCSC Genome Browser.

Transcript of video

1:11 - Zoom to a single exon.
1:55 - Adjust width of graphic display.
2:20 - Highlight a region.
2:39 - Jump to the next exon.
 
run time: 4:25


This tutorial demonstrates how to find all the single nucleotide polymorphisms in a gene using the UCSC Genome Browser.

Transcript of video

0:43 - Set up Genome Browser display to see your gene.
1:35 - Turn on the SNPs track to see SNPs in your gene.
3:27 - Get SNPs from the Table Browser.
4:36 - Load Table Browser results as a Custom Track.
 
run time: 6:13


This tutorial shows how to find all the single nucleotide polymorphisms upstream from genes using the UCSC Genome Browser.

Transcript of video

0:43 - Set up the Genome Browser display to see your gene.
2:00 - Use the Table Browser to get upstream regions.
3:38 - Paste and view your upstream regions as a Custom Track.
5:23 - Intersect upstream regions with the SNP track.
6:43 - Load upstream SNPs as a new Custom Track.
 
run time: 8:14


This tutorial will demonstrate how to find the tables in the UCSC database that are associated with the data tracks in the Genome Browser graphical viewer.

Transcript of video

0:42 - Set up the Genome Browser display.
1:18 - Turn on data tracks.
2:03 - Find a gene.
2:45 - Find tablename by mouseover.
3:38 - Find tablename by table schema: Use minibutton to access configuration page.
4:33 - Find tablename by table schema: Use track-control link to access configuration page.
4:47 - Find tablename by table schema: Click an individual item.
5:25 - Check contents with Table Browser: All fields.
6:53 - Check contents with Table Browser: Extract selected data fields.
7:25 - Download entire table.
 
run time: 8:39


This tutorial will demonstrate how to locate amino acid numbers for coding genes using the UCSC Genome Browser.

Transcript of video

0:36 - Set up the Genome Browser display.
1:35 - Open genes tracks: UCSC Genes, RefSeq, GENCODE.
2:17 - Locate your gene and zoom to an exon.
3:26 - Turn on RefSeq track coloring-by-codons.
3:51 - Zoom to codon level.
4:23 - Use minibutton for track configuration: Show codon numbering.
5:16 - Configure composite track.
5:44 - Confirm codon numbers with OMIM AV SNPs and UniProt Variants.
7:14 - View UniProt Variants details page.
 
run time: 8:02