Gene SpaghettiDepartment 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.
- Reads files in GenBank, EMBL, or FASTA format.
- Scatter-plot base usage, using a sliding Gaussian window
- Scatter-plot per-gene statistics against each other. Currently supported statistics include:
- Molecular weight
- Isoelectric point
- Base skew statistics
- Amino acid usage principal components
- Codon usage principal components
- Built in annotation browser
These views are linked. For example, selecting a scatter-plot point highlights the corresponding annotation and vice-versa.
Installing the necessary libraries on Windows is tedious but straightforward.
- Download and run the Python 2.7 Windows installer
- Download and run the mxBase Python 2.7 Windows installer
- Download and run the Numpy Python 2.7 Windows installer
- Download and run the Biopython Python 2.7 Windows installer
- Download and run the Matplotlib Python 2.7 Windows installer
- You may need to download msvcp61.dll and move it to C:\Windows\System
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.
Download the "gene-spaghetti-0.X.pyw" file above, and from the command prompt type:
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.