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Help Home > The Genome Browser > The Genome Viewer > The Protein Page > Protein Hit Tracks > Protein Alignment Tracks > The Flipped View of a Protein Page

The Flipped View of a Protein Page

This option is helpful for finding gene families. It reveals a list of translated genes in the genome that align with a target protein. (The unflipped protein page shows a list of target proteins that align with a single translated gene in the genome.) To view a flipped protein page, click a red dot below the word "Flip" on the protein page.

In this view, the protein hit information changes to report only the name and description of the target protein. Immediately beneath these are the hit tracks--now corresponding to JGI-predicted genes. You can view amino acid sequences and customize the display as with the default view.

Tracks on the Flipped Protein page include:


image A scale showing the numbering of amino acid residues in the target protein.

imageA green bar representing the target protein. Click anywhere on the bar to view the amino acid sequence for the target protein in FASTA format.

imageAlignments (grey rectangles) of translated genes with the target protein. Clicking on a grey rectangle takes you to a protein alignment report showing the detailed alignment of amino acids.

The white areas in the alignments are places where the protein has sequence but the translated gene has none, and the red areas are places where the translated gene has sequence but the target protein has none. A red hairline between grey rectangles marks the location where the sequence is missing, and the attached red rectangle just below the grey bar shows the length of the extra sequence.

The text for each track displays information about the flipped alignment.

  • start and end The coordinates of the first and last amino acids in the translated gene that align with the protein
  • len The length in amino acids of the aligned translated gene.
  • %C The percentage of the translated gene's length that is in the aligned area (% coverage).
  • %ID The percentage of the aligned area that is identical in the translated gene and the protein.
  • Score The score for the alignment.
  • [TaxName] JGI's internal ID number and name for the gene. Clicking on a description takes you to the default (unflipped) protein page for that gene.

Quick Tip

  • To return to the default view of the Protein page for a gene model (flipping the already flipped view), click the corresponding red dot below the word "Flip".