Alignment

By Dekai Wu. Handbook of Natural Language Processing, 2009

419 citations recorded by the source corpus.

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Muscle5: High-accuracy alignment ensembles enable unbiased assessments of sequence homology and phylogeny (2021, unknown): “Symmetries are enforced between x and y and between sequences and reversed sequences, giving five independent sets of probabilities for mutually exclusive alternative events: (1) transitions from the start state S (symmetric with transitions into the end state E), (2) transitions out of M, (3) trans”
CATHEDRAL: A Fast and Effective Algorithm to Predict Folds and Domain Boundaries from Multidomain Protein Structures (2007, unknown): “All three major protein classes were represented, and the quality of the alignments generated by the different structure comparison methods are measured by the score, f m , which quantiﬁes the number of amino acids correctly aligned in the structural alignment divided by the total number of aligned ”
Replacement (1980, background): “The quality of an alignment is sometimes assessed by comparison with reference alignments, such as BAliBASE (Thompson et al. , 1999), but the conclusions of such tests do not necessarily transfer to our particular usage of these programs.”
SATCHMO: Sequence Alignment and Tree Construction Using Hidden Markov Models (2003, unknown): “We used version 1 of the BAliBASE benchmark alignment database ( Thompson et al., 1999a ) as a source of reference alignments.”