PMID: 8590178Oct 1, 1995Paper

A weighting system and algorithm for aligning many phylogenetically related sequences

Computer Applications in the Biosciences : CABIOS
O Gotoh

Abstract

Most multiple sequence alignment programs explicitly or implicity try to optimize some score associated with the resulting alignment. Although the sum-of-pairs score is currently most widely used, it is inappropriate when the phylogenetic relationships among the sequences to be aligned are not evenly distributed, since the contributions of densely populated groups dominate those of minor members. This paper proposes an iterative multiple sequence alignment method which optimizes a weighted sum-of-pairs score, in which the weights given to individual sequence pairs are adjusted to compensate for the biased contributions. A simple method that rapidly calculates such a set of weights for a given phylogenetic tree is presented. The multiple sequence alignment is refined through partitioning and realignment restricted to the edges of the tree. Under this restriction, profile-based fast and rigorous group-to-group alignment is achieved at each iteration, rendering the overall computational cost virtually identical to that using an unweighted score. Consistency of nearly 90% was attained between structural and sequence alignments of multiple divergent globins, confirming the effectiveness of this strategy in improving the quality of m...Continue Reading

Citations

Oct 15, 2011·Bioinformatics·Xugang YeStephen F Altschul
Jan 19, 2013·Molecular Biology and Evolution·Kazutaka Katoh, Daron M Standley
Dec 18, 2008·Nucleic Acids Research·Stephen F AltschulYi-Kuo Yu
Oct 14, 2003·BMC Bioinformatics·G P S RaghavaGeoffrey J Barton
Oct 26, 2006·BMC Bioinformatics·Paulo A S NuinElisabeth R M Tillier
Jun 28, 2007·BMC Bioinformatics·Eric A Stone, Arend Sidow
Jan 25, 2008·BMC Evolutionary Biology·Daniel De PalmenaerJacques Mahillon
Jul 20, 2012·BMC Systems Biology·Mariko MoritaSatoru Takahashi
Jul 27, 2010·PLoS Computational Biology·Stephen F AltschulYi-Kuo Yu
Sep 1, 1997·Nucleic Acids Research·S F AltschulD J Lipman
Jul 24, 2002·Nucleic Acids Research·Kazutaka KatohTakashi Miyata
Jan 22, 2005·Nucleic Acids Research·Kazutaka KatohTakashi Miyata
May 30, 2021·BMC Bioinformatics·Nicola De MaioNick Goldman
Feb 12, 2010·Cold Spring Harbor Protocols·David W Mount

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