🔬📚 Galaxy Tool wrappers

A course on genomics and bioinformatics from WU

Galaxy RNA workbench

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.

A python package storing different tools for different NGS operations

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.

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.

An application for analysis of 5′ endpoints distribution in RNA sequencing datasets. This is particularly useful for techniques that capture 5′ monophosphorylated RNAs, such as 5PSeq, PARE-seq or GMUC. It may also be useful for ribosome profiling datasets and alike.The main workflow of fivepseq is intended for downstream analysis of alignment fi…

Jupiter Bioinformatics (V1) - To find similarities between two words, a manual comparison is required. For words between 4 and 8 letters, such a task can be performed by any of us without the use of a computer. However, what if the objects of comparison are entire phrases/sequences/files?

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 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 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.

This implementation makes a global alignment between two strings and it demonstrates the use of the global alignment algorithm.

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.

An OCaml package for predicting RNA secondary structure

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.

BRIO: a web server for RNA sequence and structure motif scan (https://doi.org/10.1093/nar/gkab400)

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 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.

These All-in-one Bioinformatics HTML5/JS files accompany the book entitled: Algorithms in Bioinformatics: Theory and Implementation, and they are compatible with all internet browsers.