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MaxEntScan for 5' and 3' splice site scoring.
Perl Matlab
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Algorithms for derivation and scoring of constrained-marginal maximum entropy distributions, with applications to 5' and 3' splice sites.

Yeo, G. and Burge, C. B. (2004). Maximum entropy modeling of short sequence motifs with applications to RNA splicing signals. J. Comp. Biol. 11, 377-394. link

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