Thank you for your question about the RepeatMasker and Conservation
tracks in the UCSC Genome Browser. You may not be seeing the repeat
or the conservation information because the RepeatMasker and
Conservation tracks are not turned on. I highly recommend taking
advantage of some the introductory resources that are available for
the browser. I would start by watching these tutorials:
. You can find information on further
training and tutorials here: http://genome.ucsc.edu/training.html
Data sets in the Genome Browser are stored in tracks. To view a
particular data set, you will need to turn on the corresponding
track. Information on repeats, such as the AluY element that you
mentioned, is contained in the RepeatMasker track. The Conservation
track contains conservation information based alignments between the
human genome and 99 different vertebrate genomes. You can use the
following steps to turn on the RepeatMasker and Conservation tracks:
1. Navigate to the gateway page for the Human/hg19 assembly,
2. In the search term box type chr16:47,662,162-47,662,468 (note
this is the position you gave for the AluY element).
3. Click Submit.
4. Scroll down the page to the section labeled Comparative
5. Click the label for the Conservation track.
6. Check the boxes next to the species that you want to be
displayed as part of this conservation track.
7. At the top of the page, set the maximum display mode for this
track to 'Full'.
8. Click Submit.
9. Scroll down the page to the section labeled Repeats.
10. Click the label for the RepeatMasker track.
11. At the top of the page, set the display mode to full.
12. Click submit.
If you have correctly turned on the RepeatMasker and Conservation
tracks, you should see some thing like this:
In this session, the first track is the UCSC Genes track showing the
PHKB gene, the second track is the RepeatMasker track showing the
AluY element, and the last track is the Conservation track showing
only the primate alignments. If you would like more information on
how the data for a track was generated, you can look at the track
description page. You can get to the description for a track by
clicking the track labels, just as you did to turn on these tracks,
and scrolling down past the track settings.
I hope this is helpful. If you have any further questions, please
reply to gen...@soe.ucsc.edu
. 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
UCSC Genome Bioinformatics Group