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Help Home > The Genome Browser > The Genome Viewer > The Protein Page > Protein Hit Tracks > Protein Alignment Tracks

Protein Alignment Tracks

To see a Protein Alignment Report showing the detailed alignment of amino acids, click a grey rectangle. The alignments are generated with the Smith-Waterman double affine algorithm.

White/light blue areas within the grey rectangles denote gaps of more than three amino acids in the translated gene sequence that do not have corresponding sequence in the matched protein.

Red areas indicate extra sequences of more than three amino acids in the matched protein that do not have a corresponding sequence in the translated gene. 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.

Quick Tips

  • To collapse all the grey tracks into one additive track, click the minus next to the green track.
  • To see a flipped view for a protein, showing all alignments of the protein with the JGI-sequenced genome, click the corresponding red dot below the word "Flip".

The text for each track displays the following information:

  • start and end The coordinates of the protein's first and last amino acids that align with the translated gene.
  • len The length in amino acids of the protein.
  • %C The percentage of the protein's length that is in the aligned area (% coverage).
  • %ID The percentage of the aligned area that is identical in the model and the protein.
  • Score The score for the alignment.

The description includes the name of the database, the ID and description of the protein, and in brackets, the organism name. To view the external database's record for that protein, click the description.