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Exploring a genomic region in Sus scrofa (Pig)

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Exploring a genomic region in Sus scrofa (Pig)

  1. Go to the region from 8,805,953 to 8,858,418 on pig chromosome 11.

  2. Configure this page to turn on the Tandem repeats (TRF) track in this view. What is this track? How many TRF overlap this region?

  3. Create a URL for this display. Email it to your neighbour.

  4. Export the genomic sequence of the region you are looking at in FASTA format.

  5. Turn off all tracks you added to the Region in detail page.

  1. Go to the Ensembl homepage. Select Pig from the drop-down menu in the blue box and enter 11:8,805,953-8,858,418 in the text box. Click Go.

  2. Click Configure this page in the left-hand menu (or on Add/remove tracks at the top left-hand corner of the Region in detail image). Type TRF into the search field in the top left-hand corner of the pop-up menu. Enable the Tandem repeats (TRF) track on the right. You can click on the i icon on the far left for a track description.

    The TRF track locates adjacent copies of a pattern of nucleotides. Save and close the new configuration by clicking on the check icon in the top right-hand corner of the pop-up menu or by clicking anywhere outside the pop-up menu. There are 19 TRF that overlap this region.

  3. Click Share this page in the left hand-side panel. Copy the URL, get your neighbour’s email address and send them the URL you copied. When you receive the link from them, open the email and click on your link. You should be able to view the page with the new configuration and data tracks they have added.

  4. Click on Export data in the left-hand menu. Leave the default parameters as they are. Click Next> and view the sequence in a new browser tab by clicking on Text. The sequence is in FASTA formatwhich comprises a header (beginning with >) that provides information about the genome assembly (primary_assembly:Sscrofa11.1), the chromosome, the start and end coordinates and the strand. For example:
    >primary_assembly:Sscrofa11.1:11:8805953-8858418:1

  5. Click on Reset configuration at the top of the Region in detail image.