Sequence Logos based on maximum values is an alternative that provides full control over how the graphics of a Sequence Logo should look like. All the inner workings of this open source application are written in native javascript. The application is independent of the internet once it is saved as a html file on the PC/Mobile phone. For input it requires an existing PPM (Position Probability Matrix), whereas the output is an image that represents the Sequence Logo. The height of each letter on a logo position is proportional to the observed frequency of the corresponding letter/symbol in the alignment column from the motif set. The letter of each stack is ordered from most to least frequent. Thus, the consensus sequence can be read from the top of the stacks. A Sequence Logo may reveal significant features of the motif set alignment that could otherwise be difficult to perceive. As such, a Sequence Logo is important for the human reader. For more detailed information, note that these native Sequence Logos in Javascript, were published in the supplementary materials of the book entitled Algorithms in Bioinformatics: Theory and Implementation. The explanations on how the code works can be found in the book's Appendix.
https://gagniuc.github.io/Sequence-Logos-based-on-maximum-values/
- Paul A. Gagniuc. Algorithms in Bioinformatics: Theory and Implementation. John Wiley & Sons, Hoboken, NJ, USA, 2021, ISBN: 9781119697961.