regarding transposable elements

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Arijita Sarkar

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Jul 23, 2015, 12:07:13 PM7/23/15
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Hello,
            I have a query regarding transposable elements. Does the hg19 repeats annotated by repeatmasker comprise all transposable elements? All repeats are not transposable elements. So,if I want to know the genomic coordinates of the transposable elements specifically, in human genome, where can I get that information? Hope you will reply soon.

Regards
Arijita

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Arijita Sarkar
Junior Research Fellow (JRF)
Centre of Excellence in Bioinformatics (COE)
Bose Institute
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Steve Heitner

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Jul 24, 2015, 1:30:04 PM7/24/15
to Arijita Sarkar, gen...@soe.ucsc.edu

Hello, Arijita.

Regarding whether or not the repeats annotated by RepeatMasker comprise all transposable elements, I don’t know that anyone can say with 100% certainty that it does, but certain RepeatMasker attempts to annotate all of them.

RepeatMasker includes a number of classes and families of repeats.  To get a list of all classes and families available and the number of items of each, you should perform a SQL query on the table on our public server.  To access our public MySQL server, follow the instructions at http://genome.ucsc.edu/goldenpath/help/mysql.html.  You should then perform the following query:

select repClass, repFamily, count(*) from rmsk group by repClass, repFamily;

From this list, you can determine which class and/or family you are interested in and search accordingly.

You can download the rmsk table (rmsk.txt.gz) in its entirety from http://hgdownload.cse.ucsc.edu/goldenPath/hg19/database/ or you can use the Table Browser to obtain only specific portions of the table.  The previously-answered mailing list question at https://groups.google.com/a/soe.ucsc.edu/d/msg/genome/kym-8GujkqI/4bSPOUqh2FwJ provides an example of how to use the Table Browser to search for items belonging to a specific class in the rmsk table.

You may also be interested in our Retroposed Genes track (http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg19&g=ucscRetroAli5).  If this track is of interest to you, you can also download ucscRetroAli5.txt.gz from http://hgdownload.cse.ucsc.edu/goldenPath/hg19/database/.

Please contact us again at gen...@soe.ucsc.edu if you have any further questions. 
All messages sent to that address are archived on a publicly-accessible Google Groups forum.  If your question includes sensitive data, you may send it instead to genom...@soe.ucsc.edu.

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Steve Heitner
UCSC Genome Bioinformatics Group

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