public track hub: human genes mapped to 99 vertebrates

[Michael Hiller]

Dear UCSC team, 

we have a trackHub (http://bds.mpi-cbg.de/hillerlab/CESAR/trackHub/hub.txt) that maps human coding genes (knownGene) to the 99 vertebrates in the hg19 100-way alignment. 

These annotations are searchable for the human gene symbol. Please find below a short summary and a preprint of the paper. 

We think these annotations are useful as (i) provide the location of the human ortholog and (ii) they provide a high-quality gene annotation for many assemblies where this is missing right now. 

Therefore, I would like to ask if this hub can be added to the list of public trackHubs? 

(In case our hub could be added to the list of Public Hubs soon, I would like to add a sentence to the paper proofs, which we expect next week).

Please let me know if I can help with anything. 

Thanks a lot

- Michael 

Summary: We have mapped human coding genes (knownGene) to the 99 vertebrates in the hg19 100-way alignment. Our mapping approach uses an HMM-based method called CESAR to realign exon sequences, considering the annotated reading frame and splice sites. The underlying HMM tries to find an alignment that shows an "intact exon" if possible. We can show that this avoids thousands of spurious frameshifts and that CESAR can detect 91% of the splice site shifts that occurred in evolution. This approach is highly accurate as 99% of the exons that lack inactivating mutations after realigning match real exons. 

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Michael Hiller, PhD

Research Group Leader

Max Planck Institute of Molecular Cell Biology and Genetics&

Max Planck Institute for the Physics of Complex Systems

Dresden, Germany

http://www.mpi-cbg.de/research/michael-hiller.html

 

[Matthew Speir]

Hi Michael,

Thank you for your request to add this track hub to our list of public hubs.

I'm really impressed with the work that you and your group have put into this. I will pass you hub along to someone in our quality assurance team for review. They will review your hub and contact you if they have any questions or suggestions. Additionally, in the meantime, I would read over our "Public Hub Guidelines" and ensure that your hub meets these minimum standards: http://genomewiki.cse.ucsc.edu/index.php/Public_Hub_Guidelines.

Unfortunately, I can't provide an estimate of when your hub will be added to the list. However, you are welcome to include the link to our hub in your manuscript. You can include instructions for loading this into the UCSC Genome Browser using the Track Hub page and the "My Hubs" tab: http://genome.ucsc.edu/cgi-bin/hgHubConnect. Or you can include a link to the Track Hub page that loads your hub automatically: http://genome.ucsc.edu/cgi-bin/hgHubConnect?hubUrl=http:/bds.mpi-cbg.de/hillerlab/CESAR/trackHub/hub.txt

You can also include a link to the Genome Browser that will automatically load the hub on the assembly of your choice. For example to load your hub on the Rat (rn5) genome, you could use a link like so: 

http://genome.ucsc.edu/cgi-bin/hgTracks?db=rn5&hubUrl=http:/bds.mpi-cbg.de/hillerlab/CESAR/trackHub/hub.txt

If you would like to change the assembly that the Genome Browser loads to, you can swap out rn5 for any UCSC database name (e.g. hg19, mm10, etc.) after the "db=" parameter in the URL above.

I hope this is helpful. If you have any further questions, please reply to gen...@soe.ucsc.edu. All messages sent to that address are archived on a publicly-accessible Google Groups forum. If your question includes sensitive data, you may send it instead to genom...@soe.ucsc.edu.

Matthew Speir
UCSC Genome Bioinformatics Group

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