1. 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...

2. Go to the genome browser...

3. Select clade and genome...

4. 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.

5. 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...

6. In the upstream promoter region there is a highly conserved region In the upstream promoter region there is a highly conserved region

7. Zoom in on this region by drawing a selection box from the top left to bottom right...

8. Click on Tables in the menu on top to go to the table browser and download the maf...

9. 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

10. 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.

11. 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...