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A 3D Objective Digital Stain is able to show the information structure of a DNA or RNA sequence in a graphical manner. In this case, the ODS is computed using the local frequency of the symbols from a sliding window. In the 3D version, the overlapping values (similar sliding windows) are represented by a gradient from black to red.
Sequence Logo - block style with axes (native Java Script) 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.
A 3D Objective Digital Stain is able to show the information structure of a DNA or RNA sequence in a graphical manner. In this case, the ODS uses the global frequency of symbols (A, T/U, C, G) from the input sequence to calculate the local frequency of these symbols from a sliding window.
Self-sequence alignment represents a novel mathematical model for measuring the information content in biological sequences, such as DNA, RNA, or proteins. Nevertheless, the use of this model is not limited to biological sequences. Thus, any symbol inside a sequence can be considered.
This implementation is an alternative that provides full control over how the graphics of a Sequence Logo should look like, and is an alternative to an application called WebLogo. 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.
A 2D Objective Digital Stain is able to show the information structure of a DNA or RNA sequence in a graphical manner. In this case, the ODS is computed using the local frequency of the symbols from a sliding window.
Simple JS implementation of Objective Digital Stain (ODS) produces ODS images from DNA sequences. On ODSs, the information content (IC) is represented vertically on the y-axis and the frequency of different letters is represented horizontally on the x-axis.
Ordered Sequence Logo based on existing matrices 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 html.
This JavaScript implementation detects the areas where two DNA sequences are complementary to each other. All symbols from UTF-8 are accepted by this algorithm.
This JavaScript implementation detects the areas where two RNA sequences are complementary to each other. All symbols from UTF-8 are accepted by this algorithm.
This is a high discrimination scanner designed to recognise DNA motifs within a long stretch of DNA. Most importantly, this implementation shows how to implement a variable sensitivity for detection, by modifying the pseudocount values.
Sequence Logo - relative style with axes 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.