Http://cs273a.stanford.edu 1 UCSC Genome Browser Tutorial The UCSC Toolset & Portal to the Human.
Downloading a multiple alignment for your region of interest from the UCSC Genome Browser ( that can...
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Transcript of Downloading a multiple alignment for your region of interest from the UCSC Genome Browser ( that can...
![Page 1: Downloading a multiple alignment for your region of interest from the UCSC Genome Browser ( that can be uploaded in ConTra for.](https://reader035.fdocuments.net/reader035/viewer/2022081518/5519b58255034660578b478f/html5/thumbnails/1.jpg)
Downloading a multiple alignment for your region of interest
from the UCSC Genome Browser (http://genome.ucsc.edu/)
that can be uploaded in ConTra for analysis...
Downloading a multiple alignment for your region of interest
from the UCSC Genome Browser (http://genome.ucsc.edu/)
that can be uploaded in ConTra for analysis...
![Page 2: Downloading a multiple alignment for your region of interest from the UCSC Genome Browser ( that can be uploaded in ConTra for.](https://reader035.fdocuments.net/reader035/viewer/2022081518/5519b58255034660578b478f/html5/thumbnails/2.jpg)
Go to the genome browser...Go to the genome browser...
![Page 3: Downloading a multiple alignment for your region of interest from the UCSC Genome Browser ( that can be uploaded in ConTra for.](https://reader035.fdocuments.net/reader035/viewer/2022081518/5519b58255034660578b478f/html5/thumbnails/3.jpg)
Select clade and genome...Select clade and genome...
![Page 4: Downloading a multiple alignment for your region of interest from the UCSC Genome Browser ( that can be uploaded in ConTra for.](https://reader035.fdocuments.net/reader035/viewer/2022081518/5519b58255034660578b478f/html5/thumbnails/4.jpg)
Search for ATOH7.This gene is not yet an annotated gene in X. tropicalis
and will not be found in ConTra. A multiple alignment
in MAF format can be downloaded from UCSC and
uploaded for analysis in ConTra.
Search for ATOH7.This gene is not yet an annotated gene in X. tropicalis
and will not be found in ConTra. A multiple alignment
in MAF format can be downloaded from UCSC and
uploaded for analysis in ConTra.
![Page 5: Downloading a multiple alignment for your region of interest from the UCSC Genome Browser ( that can be uploaded in ConTra for.](https://reader035.fdocuments.net/reader035/viewer/2022081518/5519b58255034660578b478f/html5/thumbnails/5.jpg)
Because human ATOH7 can be mapped on
the X. tropicalis genome the location is
known.
Click on zoom out 10x to look at
the upstream promoter region...
Because human ATOH7 can be mapped on
the X. tropicalis genome the location is
known.
Click on zoom out 10x to look at
the upstream promoter region...
![Page 6: Downloading a multiple alignment for your region of interest from the UCSC Genome Browser ( that can be uploaded in ConTra for.](https://reader035.fdocuments.net/reader035/viewer/2022081518/5519b58255034660578b478f/html5/thumbnails/6.jpg)
In the upstream promoter region
there is a highly conserved region
In the upstream promoter region
there is a highly conserved region
![Page 7: Downloading a multiple alignment for your region of interest from the UCSC Genome Browser ( that can be uploaded in ConTra for.](https://reader035.fdocuments.net/reader035/viewer/2022081518/5519b58255034660578b478f/html5/thumbnails/7.jpg)
Zoom in on this region by drawing a selection
box from the top left to bottom right...
Zoom in on this region by drawing a selection
box from the top left to bottom right...
![Page 8: Downloading a multiple alignment for your region of interest from the UCSC Genome Browser ( that can be uploaded in ConTra for.](https://reader035.fdocuments.net/reader035/viewer/2022081518/5519b58255034660578b478f/html5/thumbnails/8.jpg)
Click on Tables in the menu on top to go to
the table browser and download the maf...
Click on Tables in the menu on top to go to
the table browser and download the maf...
![Page 9: Downloading a multiple alignment for your region of interest from the UCSC Genome Browser ( that can be uploaded in ConTra for.](https://reader035.fdocuments.net/reader035/viewer/2022081518/5519b58255034660578b478f/html5/thumbnails/9.jpg)
Select the appropriate tracks:
» group = Comparative Genomics
» track = Conservation
» table = multiz7way (here for X. tropicalis)
» output format = MAF – multiple alignment format
Make sure the position is selected and
specify the output file name e.g. XtAtoh7.maf
Select the appropriate tracks:
» group = Comparative Genomics
» track = Conservation
» table = multiz7way (here for X. tropicalis)
» output format = MAF – multiple alignment format
Make sure the position is selected and
specify the output file name e.g. XtAtoh7.maf
![Page 10: Downloading a multiple alignment for your region of interest from the UCSC Genome Browser ( that can be uploaded in ConTra for.](https://reader035.fdocuments.net/reader035/viewer/2022081518/5519b58255034660578b478f/html5/thumbnails/10.jpg)
Save the MAF file on your computer...On Windows computers the extension .maf can be
suggested as an Access format but this may be ignored.
If another extension is used (e.g. XtAtoh7.txt) this is also
accepted by ConTra as long as the data in the file is in the
correct format.
Save the MAF file on your computer...On Windows computers the extension .maf can be
suggested as an Access format but this may be ignored.
If another extension is used (e.g. XtAtoh7.txt) this is also
accepted by ConTra as long as the data in the file is in the
correct format.
![Page 11: Downloading a multiple alignment for your region of interest from the UCSC Genome Browser ( that can be uploaded in ConTra for.](https://reader035.fdocuments.net/reader035/viewer/2022081518/5519b58255034660578b478f/html5/thumbnails/11.jpg)
The MAF file can be opened in a simple
text editor (Notepad, Wordpad, Gedit,...)
and should look like this one.
You are now ready to upload this file
in ConTra for analysis...
The MAF file can be opened in a simple
text editor (Notepad, Wordpad, Gedit,...)
and should look like this one.
You are now ready to upload this file
in ConTra for analysis...