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Go to the genome browser...

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. Select clade and genome. Search for ATOH7.

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Go to the genome browser...

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  1. Downloading a multiple alignmentforyourregion of interest from the UCSC Genome Browser (http://genome.ucsc.edu/) thatcanbeuploaded in ConTraforanalysis...

  2. Go to the genome browser...

  3. Select clade and genome...

  4. Search for ATOH7. This gene is notyetanannotated gene in X. tropicalisand willnotbefound in ConTra. A multiple alignment in MAF formatcanbedownloadedfrom UCSC and uploadedforanalysis in ConTra.

  5. Becausehuman ATOH7 canbemappedon the X. tropicalisgenome the location is known. Click on zoom out 10x to look at the upstream promoterregion...

  6. In the upstream promoterregion there is a highlyconservedregion

  7. Zoom in onthisregionbydrawing a selection box from the top left to bottom right...

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

  9. Select the appropriate tracks: » group = ComparativeGenomics » track = Conservation » table = multiz7way (herefor X. tropicalis) » output format = MAF – multiple alignmentformat Makesure the position is selected and specify the output file name e.g. XtAtoh7.maf

  10. Save the MAF file onyour computer... On Windows computers the extension .maf canbesuggested as an Access formatbutthismaybeignored. Ifanotherextension is used (e.g. XtAtoh7.txt) this is alsoacceptedbyConTra as long as the data in the file is in the correct format.

  11. The MAF file canbeopened in a simpletexteditor (Notepad, Wordpad, Gedit,...) and should look likethisone. You are nowready to uploadthis file in ConTraforanalysis...

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