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...

Go to the genome browser...Go to the genome browser...

Select clade and genome...Select clade and genome...

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.

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...

In the upstream promoter region

there is a highly conserved region

In the upstream promoter region

there is a highly conserved region

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...

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...

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

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.

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...