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perl score5.pl test5 
perl score3.pl test3

are examples of scoring 5'ss splice sites in test5, and 3'ss in test3, using the maximum entropy models for splice sites.

The MaxEnt models read in tables generated from our previous analysis to score splice sites.

Feel free to modify the perl scripts for your own purposes, but please cite
Yeo G and Burge C.B., Maximum Entropy Modeling of Short Sequence Motifs with Applications to RNA Splicing Signals,
Journal of Computational Biology, in press.

Copyright 2004, Gene Yeo, Chris Burge.