[Genome] Mouse to human orthologs

[Michael Klurfeld]

Dear UCSC Genome Bioinformatics Group,

I have a large list of mouse genes, and I would like to find the human
orthologs of these genes. I know how to find one ortholog at a time, but I
would like to find a way to find many orthologs at a time instead of having
to repeat the process used to find an individual gene hundreds of times. Do
you know any methods that I could use to accomplish this task?

Thank you,
Michael Klurfeld

[Archana Thakkapallayil]

Hello Michael,

Here are two previously answered mailing list questions with
instructions on how to extract the orthologous mouse genes for the list
of Human genes. You could follow the same steps using the 'hgBlastTab'
table in the mm8 assembly to find the human ortholog for your list of
mouse genes.

http://www.soe.ucsc.edu/pipermail/genome/2007-March/013096.html
http://www.soe.ucsc.edu/pipermail/genome/2004-October/005789.html

I hope this information is helpful to you. Please don't hesitate to
contact us again if you require further assistance.

Regards,

Archana
UCSC Genome Bioinformatics Group

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[jp d]

hi,
i was wondering if there is a way to load
a 'genome graph' track via a link
similar to the linkable custom bed files
ie
hgTracks?org=Mouse&db=mm8&position=chr2:100100000-100101500&hgt.customText=tmp

where tmp is a 'chromGraph' file
thanks,

jpd

[Archana Thakkapallayil]

Hello jpd,

You can load a 'chromGraph' into Genome Graphs by passing in a URL as
the value of the hgGenome_uploadFile variable, e.g.

...&hgGenome_uploadFile=URL..

Here is a complete link to submit:

http://www.genome.ucsc.edu/cgi-bin/hgGenome?clade=mammal&org=Human&db=hg18&hgGenome_dataSetName=dname&hgGenome_dataSetDescription=blahblah&hgGenome_formatType=best%20guess&hgGenome_markerType=best%20guess&hgGenome_columnLabels=best%20guess&hgGenome_maxVal=&hgGenome_labelVals=&hgGenome_maxGapToFill=25000000&hgGenome_uploadFile=http://hgwdev.cse.ucsc.edu/qa/archana/chromTest.txt&hgGenome_doSubmitUpload=submit

I hope this information helps. Please let us know if you have further questions.

Regards,

Archana
UCSC Genome Bioinformatics Group