A strategy for the rapid multiple alignment of protein sequences. Confidence levels from tertiary structure comparisons.

By Geoffrey J. Barton, Michael J.E. Sternberg. 1987

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Citations in the corpus

Enhancement of protein modeling by human intervention in applying the automatic programs 3D‐JIGSAW and 3D‐PSSM (2001, background): “values, between the target and best parent, and hierarchically aligned as described previously.(8) This multiple se-”
Comparative Protein Structure Modeling Using Modeller (2006, background): “Multiple alignments are generally more reliable than pairwise alignments (Barton and Sternberg, 1987; Taylor et al., 1994).”
Comparative Protein Structure Modeling Using MODELLER (2007, background): “The type of a question that can be addressed with a particular model does depend on its accuracy (Fig.”
Cascaded multiple classifiers for secondary structure prediction (2000, unknown): “Our goal, is not to argue about the best way of decomposing the 8 states of DSSP into 3 states, as we think that all these methods are defensible from a structural point of view, rather our goal is to give a complete view of the performance of Prof using different definitions.”
Matt: Local Flexibility Aids Protein Multiple Structure Alignment (2008, methodology): “We build up a single multiple structure alignment from such transformations using a similar method to that introduced by Barton and Sternberg [39].”
Improved accuracy of multiple ncRNA alignment by incorporating structural information into a MAFFT-based framework (2008, background): “(iii) Then, the initial alignment is subjected to an iterative refinement process [20,37] to maximize an objective score.”
AL2CO: calculation of positional conservation in a protein sequence alignment (2001, background): “Vast numbers of algorithms have been developed to construct multiple sequence alignments (Barton and Sternberg, 1987; Feng and Doolittle, 1987; Taylor, 1988; Lipman et al., 1989; Thompson et al., 1994a; Eddy, 1995; Gotoh, 1996; Notredame et al., 1998; Morgenstern, 1999; to cite a few).”
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.”
OXBench: A benchmark for evaluation of protein multiple sequence alignment accuracy (2003, unknown): “The accuracies of AMPS alignment based on the faster to compute PID and NAS scores for clustering were also computed and the differences summarised in Table 6 for families that contain more than two sequences (the set of Multiple Families).”
Multiple sequence alignment using partial order graphs (2002, methodology): “Many MSA methods have been developed with 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 al”