A novel randomized iterative strategy for aligning multiple protein sequences

By M. Berger, P. Munson. 1991

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Citations in the corpus

MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability (2013, methodology): “…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 Sternberg 1987; Berger and Munson 1991; Gotoh 1993; Katoh et al. 2005), and structural alignment methods for RNAs (Q-INS-i and X-INS-i; Katoh and Toh 2008a).”
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].”
ProbCons: Probabilistic consistency-based multiple sequence alignment. (2005, methodology): “To improve the alignment, we employ a randomized iterative improvement strategy (Berger and Munson 1991).”
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.”
Optimal alignment between groups of sequences and its application to multiple sequence alignment (1993, methodology): “As exemplified in Table I, the merits Five serine proteases and six insect globins were subjected to a modified randomized iterative refinement method (Berger and Munson, 1991) with and without prior progressive alignment.”
A simple method to control over-alignment in the MAFFT multiple sequence alignment program (2016, methodology): “In the iterative refinement step (Barton and Sternberg, 1987; Berger and Munson, 1991; Gotoh, 1996), the initial alignment is divided into two groups, I and J , and then the groups are re-aligned.”
MAFFT version 5: improvement in accuracy of multiple sequence alignment (2005, methodology): “In MAFFT, an initial alignment is constructed by the progressive method (6,7) and then refined by the iterative refinement method (8,9).”