want to get the sequence from my selected region

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Moonmoon Deb

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Apr 26, 2013, 8:37:08 AM4/26/13
to gen...@soe.ucsc.edu

sir
please let me know how can i download the sequence of my selected region of a chromosome
--
Thanking You with Regards.
Moonmoon Deb


Luvina Guruvadoo

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Apr 26, 2013, 3:20:26 PM4/26/13
to Moonmoon Deb, gen...@soe.ucsc.edu
Hi Moonmoon,

One way to do this is by navigating to "View" then "DNA" in the top blue
bar when viewing your assembly of interest. Here is an example for the
human (hg19) assembly:
http://genome.ucsc.edu/cgi-bin/hgc?g=getDna&i=mixed&c=chr21&l=33031596&r=33041570&db=hg19.

If you have a list of genomic coordinates, then I would recommend using
our Table Browser. If you're unfamiliar with the Table Browser, please
see the User's Guide at
http://genome.ucsc.edu/goldenPath/help/hgTablesHelp.html.

Follow the steps below (using hg19 as an example):

1. From http://genome.ucsc.edu, select "Tables" from the blue navigation
bar at the top of the screen.

2. Select the following options:
Clade: Mammal
Genome: Human
Assembly: Feb. 2009 (GRCh37/hg19)
Group: Mapping and Sequence Tracks
Track: Assembly
Table: gold
Region: Click the "define regions" button. You can either enter/paste
your regions into the text box or click "Browse" to upload a file
containing the regions
Output format: Select "sequence"

3. Click the "get output" button

4. Click the "get sequence" button

If you have further questions please feel free to contact the mailing
list again at gen...@soe.ucsc.edu.

---
Luvina Guruvadoo
UCSC Genome Bioinformatics Group
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