Optimal alignment between groups of sequences and its application to multiple sequence alignment

By O. Gotoh. 1993

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Citations in the corpus

MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability (2013, methodology): “As listed in table 1, MAFFT version 7 has options for various alignment strategies, including progressive methods (PartTree, FFT-NS-1, and L-INS-1) (Feng and Doolittle 1987; Higgins and Sharp 1988; Katoh and Toh 2007), iterative reﬁnement methods (FFT-NS-i, L-INS-i, E-INS-i, and G-INS-i) (Barton and”
Finding weak similarities between proteins by sequence profile comparison. (2003, methodology): “For example, in the progressive and iterative multiple alignment methods two groups of sequences have been compared using the weighted ‘sum of pairs’ score ( 12 ,13).”
Application of the MAFFT sequence alignment program to large data—reexamination of the usefulness of chained guide trees (2016, methodology): “It is known that the iterative reﬁnement technique (Barton and Sternberg, 1987; Berger and Munson, 1991; Gotoh, 1993) improves the accuracy of an MSA in comparison with the progressive method.”
Metrics and Similarity Measures for Hidden Markov Models (1999, background): “These models do not strictly follow the profile architecture and consequently cannot be compared using profile ’align-ment (Gotoh 1993).”
Recent developments in the MAFFT multiple sequence alignment program (2008, methodology): “Various combinations of objective functions and optimization strategies have been proposed to date [55–61].”
COMPASS: a tool for comparison of multiple protein alignments with assessment of statistical significance. (2003, methodology): “BLOSUM62). lu derived from equation ( 12 ) depends only on the residue composition of the profiles or sequences.”
MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform. (2002, methodology): “To overcome this difﬁculty, various heuristic methods, including progressive methods (3) and iterative reﬁnement methods (4–6), have been proposed to date.”
Multiple sequence alignment using partial order graphs (2002, background): “…different advantages and disadvantages (Taylor, 1986; Barton and Sternberg, 1987; Altschul, 1989; Lipman et al., 1989; Subbiah and Harrison, 1989; Gotoh, 1993, 1996; Thompson et al., 1994; Notredame et al., 2000; Gordon et al., 2001), but globally optimal alignment of larger numbers of sequences…”
OXBench: A benchmark for evaluation of protein multiple sequence alignment accuracy (2003, unknown): “Gotoh [17] assessed the multiple sequence alignment method CLUSTALW [8]; and four of his own methods [18–20], on 54 families from the Joy 3.2 database [21] of alignments from 3D structure comparisons.”
MAVID: constrained ancestral alignment of multiple sequences. (2003, methodology): “Iterative reﬁnement, the process of re-aligning across an edge in the tree, ﬁts in naturally with our framework [Gotoh 1993, Gotoh 1996].”