Gene Spaghetti

Gene Spaghetti is GPL software for visualizing base and amino acid usage in a genome. It was developed to visualize the unusual amino acid and base usage of Mycobacteria marinum, for the Mycobacteria research group in the Department of Microbiology at Monash University.

Gene Spaghetti requires Python, Numpy, mxBase, BioPython, and Matplotlib. It has been tested on Linux, Windows, and MaxOS X. Installing these libraries under Linux and Windows is straightforward, installing them on MacOS X is possible but somewhat involved.

Features

These views are linked. For example, selecting a scatter-plot point highlights the corresponding annotation and vice-versa.

Download

Installation

Windows:

Installing the necessary libraries on Windows is tedious but straightforward.

Now download and run the "gene-spaghetti-0.X.pyw" file above.

By the way, you've just installed a great environment for doing Bioinformatics.

Linux:

Gene Spaghetti requires Python, Numpy, BioPython, and Matplotlib. Install these using your distribution's package manager.

Download the "gene-spaghetti-0.X.pyw" file above, and from the command prompt type:
python gene-spaghetti-0.X.pyw

Mac OS X:

Find your local UNIX guru. Give him your computer. In a few days he will either have installed Gene Spaghetti or gone insane from battling with Fink.