rna

🔬📚 Galaxy Tool wrappers

A course on genomics and bioinformatics from WashU

Galaxy RNA workbench

Jupiter Bioinformatics is a browser-based tool for interactive pairwise sequence alignment and heatmap visualization. Built on the Smith-Waterman local alignment algorithm, it renders the full scoring matrix as a color-coded heatmap on an HTML5 canvas, no installation, no server, no dependencies. Open the file and start aligning.

These Bioinformatics HTML5/JS files accompany the book entitled: Algorithms in Bioinformatics: Theory and Implementation, and they are compatible with all internet browsers. These algorithms include more than 120 open-source implementations that describe many known or novel algorithms in Bioinformatics.

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 JavaScript implementation detects the areas where two DNA sequences are complementary to each other. All symbols from UTF-8 are accepted by this algorithm.

These Bioinformatics HTML5/JS files accompany the book entitled: Algorithms in Bioinformatics: Theory and Implementation, and they are compatible with all internet browsers. These algorithms include more than 120 open-source implementations.

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.

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.

BioAlign is a self-contained, browser-based tool for Smith–Waterman local sequence alignment and interactive heatmap visualization. It supports DNA, RNA, protein, numeric, and ASCII sequences, with customizable scoring, themes, local storage, fullscreen mode, and PNG/FASTA export.

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.

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.

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.

This is an application designed in HTML5/Javascript of a scanner that makes a comparison between two methods, namely between Shanon entropy (Information entropy) and self-sequence alignment (Information content). Information entropy (IE) and Information content (IC) are two methods that quantitatively measure information.

This JavaScript implementation detects the areas where two DNA/RNA/protein sequences are similar to each other. All symbols from UTF-8 are accepted by this algorithm.

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.

A python package storing different tools for different NGS operations

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.

Sequence Logos using logarithms 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.