[Genome] Why is the "HMR Conserved Transcription Factor Binding Sites" track only available for the human genome?

[Matt Weirauch]

Hi David,

There currently is only a conserved binding site track for the human
genome.  A few people have recently been asking about the
syntenic site in mouse and rat, so I think at the very least future
tracks will incorporate this information into the humam track.

For now, if you need to find the genomic locations on mouse and rat for
only a few sites, one way is to use the "Conservation" track showing the 8-way
alignments.  Zoom in to the region of interest and click on the alignment
itself.  This will bring you to a page giving the genomic locations in the
other species.

If you need to do this for a lot of sites, you can download the .maf
alignments that were used for the track.  You can then find the position in
that file in human and go straight down the column in the alignment to
find the position in mouse or rat.  If you need help doing this, I would
be more than happy to lend my assistance.

Matt



On Thu, 14 Jul 2005, Steffen, David wrote:

> Howdy!
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> A question from a grateful and enthusiastic user of the UCSC browser:
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> The "HMR Conserved Transcription Factor Binding Sites" track is available for hg17 and hg16 but not for mm6, mm5, rn3, or rn2.
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> The reason I find this puzzling is that the description of the "HMR Conserved Transcription Factor Binding Sites" is "This track contains the location and score of transcription factor binding sites conserved in the human/mouse/rat alignment."  This implies to me that the binding sites must have
> been looked-at (and thus localized) on mouse and rat, so why not make this data available?  Perhaps I am misunderstanding what is being said here, perhaps finding the site on the alignment is not the same as finding it on the mouse and rat genomes.  Could someone enlighten me?
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> Given the above, is there a relatively straightforward and precise way of taking the location of the sites on human and using the alignment to find the coordinates of the syntenic site on mouse and human?
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> THANKS!!
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> David Steffen, Ph.D.
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> Director, Bioinformatics Research Center
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> Professor, Molecular and Human Genetics
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> Baylor College of Medicine
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>