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===== Converting Uppercase to Exons Example: NRF1 =====
Some genome browser tools such as the [[http://genome.ucsc.edu/|UCSC Genome Browser]] allow you to download a genomic sequence and specify introns as lowercase.  pLOT can use this to automate annotating of exons from sequences formatted in this manner.  For example, to annotate the exons of NRF1:

1. Go to the UCSC Genome browser and select the human genome.

{{::ucsc_1.png?400|}}

2. Enter NRF1 in the text box and click the dropdown window with the name.  Then click the "go" button.

{{:ucsc_2.png?400|}}

3. Click the transcript of your choosing in the display window.  In this example we will use variant 1.

{{:ucsc_3.png?400|}}

4. Under the Sequence and Links to Tools Database section, click the link labeled "Genomic Sequence" and the coordinates of the transcript.

{{:ucsc_4.png?400|}}

5. Make sure the CDS Exons and the Introns options are selected and that the "Exons in upper case, everything else in lower case." option is selected below and click the "submit" button to retrieve the sequence.

{{:ucsc_5.png?400|}}

6. Open a new pLOT window, click the "File>New Project" menu item and paste the sequence.  Click the OK button.  Click the Toggle Circular/Linear button to show the sequence as linear (this step is not necessary for annotating the introns but we'll do it anyway since it is a linear chromosome).

{{:cirlinbutton.png|}}

7. Finally, go to the Tools menu and click the "Convert Uppercase to Exons" menu item.  Exons will be automatically annotated numerically.

{{:convertintron.png?400|}}
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