Query regarding repeat element display match with sequence
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roshan fatima
May 15, 2014, 8:22:49 AM5/15/14
to gen...@soe.ucsc.edu
Dear genome team
lately I am finding a problem in matching the sequence with its conservation/ repeat elements
in human genome.
For example, for the region I am interested in an intron of PHKB gene, the DNA for repeat
element AluY is given as 47662162 to 47662468 in hg19/ grc37. But when I submit a genomic
sequence that starts way upstream of AluY but ends with the breakpoint of AluY, say
chr16:47660000-47662500, this segment does not show the Alu repeat neither its conservation or
lack of it.
Could you please look into the matter? There seems to be a mis match between the sequence
given and the repeats shown in that sequence.
Thanking you,
sincerely,
Dr. Roshan Fatima
CBL,
MBGU,
JNCASR
Bangalore 64.
lately I am finding a problem in matching the sequence with its conservation/ repeat elements
in human genome.
For example, for the region I am interested in an intron of PHKB gene, the DNA for repeat
element AluY is given as 47662162 to 47662468 in hg19/ grc37. But when I submit a genomic
sequence that starts way upstream of AluY but ends with the breakpoint of AluY, say
chr16:47660000-47662500, this segment does not show the Alu repeat neither its conservation or
lack of it.
Could you please look into the matter? There seems to be a mis match between the sequence
given and the repeats shown in that sequence.
Thanking you,
sincerely,
Dr. Roshan Fatima
CBL,
MBGU,
JNCASR
Bangalore 64.
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Matthew Speir
May 16, 2014, 7:11:37 PM5/16/14
to roshan fatima, gen...@soe.ucsc.edu
Hello Roshan,
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: http://www.openhelix.com/ucsc. 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, http://genome.ucsc.edu/cgi-bin/hgGateway?db=hg19.
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 Genomics.
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: http://genome.ucsc.edu/cgi-bin/hgTracks?hgS_doOtherUser=submit&hgS_otherUserName=mspeeeer&hgS_otherUserSessionName=hg19_mlqAluYcons. 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 genom...@soe.ucsc.edu.
Matthew Speir
UCSC Genome Bioinformatics Group
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: http://www.openhelix.com/ucsc. 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, http://genome.ucsc.edu/cgi-bin/hgGateway?db=hg19.
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 Genomics.
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: http://genome.ucsc.edu/cgi-bin/hgTracks?hgS_doOtherUser=submit&hgS_otherUserName=mspeeeer&hgS_otherUserSessionName=hg19_mlqAluYcons. 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 genom...@soe.ucsc.edu.
Matthew Speir
UCSC Genome Bioinformatics Group
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