[Genome] Microsatellite markers

[Rachel Harte]

Dear Tom Lindner,

The STS markers track has markers from the Marshfield and deCODE maps. If
you go to the hg18 (Build 36.1) Genome Browser and scroll to the "Mapping
and Sequencing Tracks" section and then click on the link for STS markers,
you will see a description of the track. The information on the mapped
location and the position (in cM) is in the stsInfo2 table. This can be
downloaded either from our Downloads server:

http://hgdownload.cse.ucsc.edu

and follow the "Human" link and select "Annotation database" to see all
the tables for that assembly.
Alternatively, if you click on the "Tables" link on the top blue bar, you
can use the Table Browser to obtain information from this table. There is
also a Microsatellite track in the "Variation and Repeats" group so you
could perhaps do an intersection of the STS marker track with the
microsatellite track to find the microsatellites in the STS marker track.
This can be done using the Table Browser. The Microsatellite track was
created by taking a subset of the Simple Repeats track (created using the
Tandem Repeats Finder program).  The Microsatellites in this track are
those repeats of period 2 or 3 with 100% identity and no indels and with
at least 15 copies of the repeat.

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

Rachel

Rachel Harte
UCSC Genome Bioinformatics Group
http://genome.ucsc.edu


On Mon, 15 Jan 2007, Tom H. Lindner wrote:

> Dear Sir/Madam,
> Is there any chance to get a list (simple text) of all microstellite markers
> in the human genome including physical positions from NCBI build 36.1? cM
> positions from Marshfield, SLM1, and deCODE in addition would be even
> better. Unfortunately, I was not able to download such a table from your
> webiste.
> Thanks in advance, Tom Lindner.
>
>
> University of Erlangen-Nuremberg
>
> Department of Nephrology and Hypertension
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> Community Hospital Nuremberg
>
> Tom H. Lindner, M.D., Ph.D.
>
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