To display the Sequence Logo track:

To display or hide the Sequence Logo track in the Sequences view footer, perform an alignment and then check or uncheck the Sequence Logo box in the Tracks panel. This box is only visible after performing an alignment.

How Sequence Logo is calculated:

The Sequence Logo is a visualization of the nucleotide or amino acid at a given position, based on a formula for the Shannon uncertainty measure given by Schneider and Stephens (1990). The height ranges from 0-2 for nucleotides and 0-4.3 for proteins, and the height of each letter code is proportional to its frequency. The most common letter code is at the top of each position.The accuracy of this calculation is proportional to the number of sequences in the alignment, and the track may not be displayed if there are too few sequences.

To avoid implying conservation in the presence of gaps, the Sequence Logo algorithm adjusts the height of the letter stack such that the total height of the symbols is multiplied by the fraction (# of residues / (# of residues + # of gaps)).

Hover over the logo to reveal a tooltip with the information content of each letter at the position.

To change Sequence Logo options:

To learn how to access the options section for this track, see Tracks.

When there are relatively few sequences without gaps represented at a given position, we recommend checking Small sample correction . This correction has no effect when there are sufficient numbers of sequences to provide a good estimate of information content.

Click if you wish to return to the default values.

Need more help with this?

Thanks for your feedback.