Proteome browser?

[Michael Shamblott]

As a long time user of your great genome browser, I have a very basic question.  I am trying to analyze protein domains of several human proteins such as MAGEA1, TYR, TP53.  When the protein has a single coding exon, I get the information I need, which includes all the annotations, aligned as tracks below the protein.  However, when interrupted by introns, the protein is displayed (correctly) as a series of blocks, which is fine when preparing a gene-based figure,  but I need to show the protein as a contiguous block.  I have read about UCSC proteome browser, but I cannot figure out how to access it from the genome browser. 

 

Michael J. Shamblott, Ph.D.

Chief Scientific Officer

Morphogenesis, Inc.

10500 University Center Drive, Suite 110

Tampa, FL 33612

Phone: 813 875 6600 ext 103

 

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[Luis Nassar]

Hello, Michael.

Thank you for your interest in the Genome Browser.

Regarding the UCSC Proteome Browser, that project is now retired. However, we should be able to accomplish what you are asking for with our "Multi-Region Display" feature (http://genome.ucsc.edu/goldenPath/help/multiRegionHelp.html).

You can find the multi-region button located next to the chromosome position and the search bar above the tracks image (http://genome.ucsc.edu/cgi-bin/hgTracks?db=hg38). You can then select to split the image on exons only (this will use the default genes track for the assembly, currently GENCODE V36 for hg38). Then submit.

Here is a session looking at MAGEA1 displaying only exons with no padding: http://genome.ucsc.edu/s/Lou/RM27332

One thing to note is that using the default models also includes pseudogenes (http://genome.ucsc.edu/s/Lou/TYRmultiRegion). If you would like to remove these, you can use the Table Browser (http://genome.ucsc.edu/cgi-bin/hgTables) to generate a bed file to pass to the Multi-Region Display. Let us know if you would like to learn more about this approach.

I hope this is helpful. Please include gen...@soe.ucsc.edu in any replies to ensure visibility by the team. All messages sent to that address are archived on our public forum. If your question includes sensitive information, you may send it instead to genom...@soe.ucsc.edu.

Lou Nassar
UCSC Genomics Institute

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