A fast, flexible system for detecting splice sites in the genomic DNA of various eukaryotes. The system has been trained and tested successfully on Plasmodium falciparum (malaria), Arabidopsis thaliana, human, Drosophila, and rice . Training data sets for human and Arabidopsis thaliana are included. See below for instructions on downloading the complete system including source code .
GeneSplicer is released as source code and was tested on Linux RedHat 6.x+, Sun Solaris, and Alpha OSF1, but should work on any Unix system.
This software is OSI Certified Open Source Software.
% tar -xzf GeneSplicer.tar.gz
A directory named 'GeneSplicer/' will be created which contains the executable, training data sets, and other supporting files.
Training data sets are included in the tar file.
Training GeneSplicerThere is no independent program to train GeneSplicer, but there is a way to obtain the necessary files by using the training procedure of GlimmerHMM, which can be downloaded from here.
After running trainGlimmerHMM, create a directory with the following files from the resulted GlimmerHMM training directory:
In the same directory, create a file called config_file with the following
info on a line, in this order:
You can contact us about GeneSplicer at: mpertea jhu edu
M. Pertea , X. Lin , S. L. Salzberg . GeneSplicer : a new computational method for splice site prediction . Nucleic Acids Res . 2001 Mar 1;29(5):1185-90 .