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.
The Y-axis describes the amount of information in bits*.
The X-axis shows the position in the alignment.
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.
The chosen formats plus the raw eps and the weight matrix is downloadable through the links in the top left corner.
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.
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.
The Shannon Logo
The Kullback-Leibler Logo, this logo type is the default of Seq2Logo. It gives a clear visual image of the conserved and variable regions, while also depicting depleted amino acids.
The Weighted Kullback-Leibler Logo, focusses on providing more information about the amino acid enrichment and depletion, instead of the probability, by altering the height of the individual amino acid to correspond to their log-odds score.
The Probability Weighted Kullback-Leibler Logo, this logo is a mixture of regular Kullback-Leibler and Weighted Kullback-Leibler, where the height of the amino acids corresponds to their probability times their log-odds score, which is also the information contribution of the amino acid. This logo really emphasizes the important parts.
The PSSM Logo, this logo type depicts the scoring matrix directly as it is, with no regards to the information centent. This logo has the advantage of clearly visualizing amino acid depletion at unconserved regions, and can be usefull to locate specific depletions such as the N-linked glycosylation sites with motif N-X-S/T, where X can be any amino acid but proline.
The Raw Logo, this shows a clean Kullback-Leibler logo without use of neither sequence weighting nor pseudo counts.
This logo is the same as the raw logo, but the redundancy in dataset has now been reduced by the use of the Hobohm 1 algorithm (sequence weighting method).
This logo is the same as the sequence weighted logo, but a pseudo counts method has been applied to correct for the lack of occurrences, due to a small dataset.
This logo shows the effect (shrinks the width of the stack) of gaps starting with 0% gaps and ending up with 90% gaps. In advanced options the user has the ability to set a minimum stack width. If this is set to 1 it will disable the shrinking effect. The default value is 0.5 (50%).