Prokaryotic gene prediction
Given a prokaryotic DNA sequence, predicts genes using GLIMMER algorithm
Implements a reasonably faithful implementation of the GLIMMER algorithm for prokaryotic gene predict, as described in:
Delcher, Arthur L., et al. "Improved microbial gene identification with GLIMMER." Nucleic acids research 27.23 (1999): 4636-4641.
The primary departure is that it does not take the frame positions of bases into account.
Run Instructions:
Example input data is found in dna.fna. Data input and output are in this format.
Run svm_gp.java. The program assumes it is being initialized at "Gene Predict/"
Note that the program makes use of the Apache Commons Math library, in order to implement the chi square test.