CONTRAlign (CONditional TRAining for Protein Sequence Alignment)is an extensible and fully automatic parameter learning framework for protein pairwise sequence alignment based on pair conditional random fields. The CONTRAlign framework enables the development of feature-rich alignment models which generalize well to previously unseen sequences and avoid overfitting by controlling model complexity through regularization.
Chuong Do (firstname.lastname@example.org)
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Do, C.B., Gross, S.S., and Batzoglou, S. (2006)
CONTRAlign: Discriminative Training for Protein Sequence Alignment.
In Proceedings of the Tenth Annual International Conference on Computational Molecular Biology (RECOMB 2006).