swMATH ID: 8305
Software Authors: Do, Chuong B.; Gross, Samuel S.; Batzoglou, Serafim
Description: Contralign: discriminative training for protein sequence alignment. In this paper, we present CONTRAlign, an extensible and fully automatic framework for parameter learning and protein pairwise sequence alignment using pair conditional random fields. When learning a substitution matrix and gap penalties from as few as 20 example alignments, CONTRAlign achieves alignment accuracies competitive with available modern tools. As confirmed by rigorous cross-validated testing, CONTRAlign effectively leverages weak biological signals in sequence alignment: using CONTRAlign, we find that hydropathy-based features result in improvements of 5-6
Homepage: http://contra.stanford.edu/contralign/
Related Software: RNAforester; LIBLINEAR; MAFFT
Cited in: 4 Publications

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