pseudogene match

[Lucia Guidugli]

Hello, if I have a list of protein coding genes, is there a way I can upload them as a batch on genomebrowser to verify if they have homology to pseudogene and download the pseudogene's list as vcf file?

Thanks,

Lucia

[Luis Nassar]

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Hello Lucia,

Thank you for your interest in the Genome Browser.

We do not currently have a direct way to match pseudogenes to parent genes. Our main gene annotation GENCODEv32 (hg38) track offers pseudogene annotations, but does not contain parent gene information (http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg38&c=chrX&g=knownGene).

One option is to use blat (http://genome.ucsc.edu/cgi-bin/hgBlat) to query the protein sequences and match non-primary hits with pseudogenes. This would be fairly time consuming, even though blat can be run locally, and would require some inference for every protein.

You may be able to find a more streamlined solution using external resources. One example would be http://www.pseudogene.org/, which offers a list of transcript and parents using Ensembl (GENCODE) IDs (http://www.pseudogene.org/psidr/similarity.dat). They also offer files in other formats such as pseudogene position and DNA sequence. Keep in mind these are resources external to UCSC, and we offer no assurance on the data or methods.

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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