Output Format


Once the Seq2Logo server has finished running the job you submitted it will show an image file containing the logo. This logo describes the information content of the alignment file you submitted.

  1. The Y-axis describes the amount of information in bits*.
  2. The X-axis shows the position in the alignment.
  3. At each position there is a stack of symbols representing the amino acid. Large symbols represent frequently observed amino acids, big stacks represents conserved positions and small stacks represents variable positions.
  4. The chosen formats plus the raw eps and the weight matrix is downloadable through the links in the top left corner.
  5. By clicking the "show" link next to the "Warning!" sign, a list of the warnings will be shown. This will tell the user if any problem occurred, which might compromise the quality of the logo.
  6. By clicking the "show" link next to the "Settings:" sign, a list of the user specified settings, which was used in the creation of the logo, will be shown.

* You can rename the Y-axis unit to what you prefer, but for all logos except of PSSM-logo the true unit is the bit content.



There are multiple logo types which influence the visual output. Click to show these different outputs here:

There are also a few methods which influence the visual output. These different outputs are shown here.

An alignment with gaps is handled by ignoring the gaps when calculating frequencies, and by shrinking the width of the stack according to the gap percentage.

Shannon Logo

The Shannon Logo