Genome to Function 1. View Protein Sequence & its Coding DNA

  1. Load sequence alignment, select File ⇒ Input Alignment ⇒ From URL in the desktop menu and enter https://www.jalview.org/tutorial/unaligned.fa and click OK.

  2. Load annotation, select Web Service ⇒ Fetch DB References ⇒ From EMBL to UNIPROT ⇒ UNIPROT.

  3. To toggle the sequence features on and off, select View ⇒ Show Sequence Features in the alignment menu.

  4. To view the feature types, select View ⇒ Feature Settings… and this opens the Sequence Feature Settings dialog box . Click OK to close it.

  5. Select Calculate ⇒ Get Cross-References ⇒ EMBLCDS in the alignment menu. This step can take a little time, progress is indicated in the status bar.

  6. The Protein-CDS split-screen window opens. The coding DNA is located in the upper panel and the protein products are located in the lower panel.

  7. Move the mouse cursor along the amino acid residues in a protein sequence, and view the codons highlighted by the black box in the DNA alignment above it.

Note: If Jalview feels sluggish, move the windows so they don't overlap each other or minimise (but do not close!) the original locus/transcript alignment.

 This exercise can be viewed in the Genome to Function Video 1 - View Protein Sequence & its Coding DNA video.