[Genome] Downloading alignments/conservation score from the Conservation track

[Maqbool, Nauman]

Dear UCSC team

I am working on finding regulatory regions in mouse and have a dataset
of 150 genes. I downloaded -10kb to +1kb genomic region using your
browser and then scanned those sequences for the presences of some known
patterns.

I now want to have a look at the conservation of the found patterns (and
the surrounding genomic region) in other vertebrates. Is there a way I
can download multiz alignments (from 10-way multiz vertebrate alignment
track) given mouse build 34 genomic coordinates of the sequences I have?
Or, still better, can I get some sort of conservation score for each
base position for the mouse 11kb region for each of those 150 genes?

Another problem is that as I am working with a dataset of 150 genes, a
bit too much for manually downloading alignments/score, so any help on
the batch processing of such downloads would be highly appreciated.

Regards

Nauman

_______________________

Nauman J Maqbool PhD
T +64 3 489 9031
E nauman.maqbool at agresearch.co.nz
Invermay Agricultural Centre
Puddle Alley, Private Bag 50034
Mosgiel, New Zealand
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[Jennifer Jackson]

Hi Nauman,
One way to retrieve this data is by using the Table browser tool
("Tables" in blue navigation bar).

Suggested method:
1) create a custom track containing your regions of interest.
http://genome.ucsc.edu/FAQ/FAQcustom
2) run a Table browser query with the Conservation track as a query with
an intersection against this custom track
3) only regions in common will be in the output

Another way to is to ftp the Conservation track's text files and to
perform the intersection using your own tools. The same tables that you
see associated with the track in the Table browser will be on our
downloads server: http://hgdownload.cse.ucsc.edu/downloads.html

A detailed description of the data points in the conservation track are
available on the track's details page (including paper's and other
references). View this by clicking on the track label from within the
database's browser. The format of the tables themselves are described in
the Table browser using the "View table schema" link.

Please let us know if you need more detailed instructions,
Jen

--
Jennifer Jackson
UCSC Genome Bioinformatics Group

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