How can I access the "orientation" of the LCRs on Segmental Duplication?

[Samuel Fernandes]

On the results of my search on Segmental duplication (Duplications of >1000 Bases of Non-RepeatMasked Sequence); I noticed that there are some "orientation" on the LCRs. Some of them seems to go to the right and some to the left.
And I could not find how to retrieve this information.

arr[hg19] Xq28(153,429,330-153,527,982)

chrX:153481277 >>>>>>>>>>>>>>>>                             chr1:245292435<<<<                                      chrX:153564285<<<<<<<<<<

                                               chrX:153444157>>>>>>>>>>>>>>>>>

Since now, thank you very much,

Samuel Fernandes

[Jonathan Casper]

Hello Samuel,

Thank you for your question about the orientation of items in the Segmental Dups track. Information about the orientation of individual duplication sites can be found by clicking on the site in the browser. On the resulting page, the value of the "Other Position Relative Orientation" field will indicate whether the sequence is on the opposite strand in the duplicate location. + means the same strand, - means the opposite strand. The orientation arrows that you describe are a visual representation of this information - arrows pointing toward the 5' end of the chromosome (usually to the left) have a duplicate on the opposite strand. You can also retrieve this information using the UCSC Table Browser with the following steps (using the hg19 human assembly as an example):

1. Open the UCSC Table Browser at http://genome.ucsc.edu/cgi-bin/hgTables.
2. Select the following options:

clade: Mammal
genome: Human
assembly: Feb. 2009 (GRCh37/hg19)
group: Repeats
track: Segmental Dups
table: genomicSuperDups

3. If there is a specific region you are interested in, set the region to "position" and enter it into the text box. Otherwise, select "genome".
4. Select the output format "selected fields from primary and related tables".
5. Click "get output".
6. On the new page, check the boxes for "chrom", "chromStart", "chromEnd", and "strand".
7. Click "get output".

The results should provide you with a list of the chromosome locations of segmental duplications and + or - strand values. Again, records with a strand of + are found on the same strand in the duplicate location. Records with a strand of - are found on the opposite strand in the duplicate location. More information about the track can also be found on the track description page at http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg19&g=genomicSuperDups. Clicking the "View table schema" link on that page (or clicking the "describe table schema" button on the UCSC Table Browser) will provide a description of each field in the table.

I hope this is helpful. If you have any further questions, please reply to gen...@soe.ucsc.edu or genome...@soe.ucsc.edu. Questions sent to those addresses will be archived in publicly-accessible forums for the benefit of other users. If your question contains sensitive data, you may send it instead to genom...@soe.ucsc.edu.

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Jonathan Casper
UCSC Genome Bioinformatics Group

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