[Genome] question about data from Human Genome Annotation

[Hiram Clawson]

Good Morning Miguel:

There are several methods you can use to extract this information
from the UCSC Genome browser.

1.  From the chr*_rmsk.txt.gz files from the database:
	http://hgdownload.cse.ucsc.edu/goldenPath/hg18/database/chr*_rmsk.txt.gz
         or: ftp://hgdownload.cse.ucsc.edu/goldenPath/hg18/database/chr*_rmsk.txt.gz
2.  From the "Tables" browser with a filter "Alu%" on the repName or repFamily columns
3.  Directly from the MySQL server with a shell script, for example:
mysql --user=genome --host=genome-mysql.cse.ucsc.edu -A \
         -N -e "SELECT chrom FROM chromInfo;" hg18 | while read CHR
do
     mysql --user=genome --host=genome-mysql.cse.ucsc.edu -A \
         -N -e 'SELECT
genoName,genoStart,genoEnd,repName,swScore,strand,repClass,repFamily
FROM '${CHR}'_rmsk
WHERE repName LIKE "Alu%"
OR repFamily LIKE "Alu%"
' hg18
done

 From that information, you can run an analysis of the density of these elements
for your research.

--Hiram

Miguel.Gallach at uv.es wrote:
> Dear Mr/Ms,
> 
> We are analyzing few aspects of methylation in Alu repeats. We need to 
> know the distribution of each Alu subfamily in the human genome. We 
> just find the output table from the program REPEATMASKER. Do you have 
> any table summing up the densities and/or distribution in the human 
> genome of the Alu subfamilies?
> 
> Thank you very much for your attention,
> 
> Miguel
> --
> ********************************
> miguel.gallach at uv.es
> ********************************
> Miguel Gallach Caballero
> Laboratorio de Genómica Comparativa
> Departamento de Genética
> Universidad de Valencia
> 
> Calle Doctor Moliner, 50
> Burjassot 46100 (Valencia)
> SPAIN
> 
> 
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