Hi Katarina,
Your file contains data that was created some time ago by Adam Siepel
while at UCSC, now at Cornell University. It is based on some assemblies
and processes that have since been updated.
I would recommend going directly to our browser home page, accessing the
most recent assemblies of interest, and using the most recently
generated conservation data.
For human, this would be Mar. 2006 (hg18). In the track grouping
"Comparative Genomics" we have a brand new 44-way conservation track,
"Conservation". Click on the track name to see how it was generated. It
does include dog. There are multiple options for filtering/viewing data
and a very detailed methods section that should address your questions
regarding how to interpret scores and other values.
For dog, this would be May 2005 (canFam2). The "Conservation" track for
this genome includes Dog/Human/Mouse/Rat (but please note that the
databases are not the most current for human, mouse or rat).
The data files for both can also be downloaded by clicking through links
on each track's description page (click on track name to view
description/methods/references) or by going our downloads site
("Downloads" link on the side blue bar on main UCSC genome web page
http://genome.ucsc.edu/).
File formats are generally described in the README files in each directory
For dog the file is:
http://hgdownload.cse.ucsc.edu/goldenPath/canFam2/phastCons4way/
Which includes a link to format descriptions:
http://genome.ucsc.edu/goldenPath/help/phastCons.html
Some help with ftp:
http://genome.ucsc.edu/FAQ/FAQdownloads#download1
I hope this help you to find the information you were looking for, but
please let us know if you need help interpreting any specific data,
Jennifer Jackson
UCSC Genome Bioinformatics Group
Katarina Truve wrote:
> I have a question about the provided files with conserved elements. I
> downloaded a file named vertebrateAll.bed and I would like to know if
> it is
> correct that the value most to the right is the lod value? I also
> wonder what the tmp. value represents?
> Finally it would be very helpful for me if it i possible to get this
> kind list for the dog genome. Could I found and download it somewhere?
> Thanks
> Katarina Truvé
> Katarina Truvé
> Dept. Animal Breeding and Genetics
> Swedish University of Agricultural Sciences (SLU)
> P.O. Box 597, S-75124 Uppsala, Sweden
> [email protected]
>
>
>
>
>
>
> _______________________________________________
> Genome maillist - [email protected]
> http://www.soe.ucsc.edu/mailman/listinfo/genome
>
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