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Theoretical determination of amino acid substitution groups based on qualitative physicochemical properties. Available at http://cmgm.stanford.edu/biochem218/Projects%202001/Yu.pdf
, 2001
"... This paper introduces a novel method for theoretical determination of amino acid substitution groups. The method here involves making a binary matrix based on 48 qualitative physicochemical properties and calculating a substitution matrix based on this using dot products. Isolated groups with high s ..."
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This paper introduces a novel method for theoretical determination of amino acid substitution groups. The method here involves making a binary matrix based on 48 qualitative physicochemical properties and calculating a substitution matrix based on this using dot products. Isolated groups with high scores are determined to be valid substitution groups and conserved groups are derived from these valid groups. 258 valid groups and 31 conserved groups are found.
Contextual Alignment of Biological Sequences (Extended Abstract)
, 2002
"... Anna Gambin, Sl/awomir Lasota, Radosl/aw Szklarczyk, Jerzy Tiuryn and Jerzy Tyszkiewicz Institute of Informatics, Warsaw University, Banacha 2, 02097, Warsaw, POLAND ABSTRACT We present a model of contextual alignment of biological sequences. It is an extension of the classical alignment, in wh ..."
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Anna Gambin, Sl/awomir Lasota, Radosl/aw Szklarczyk, Jerzy Tiuryn and Jerzy Tyszkiewicz Institute of Informatics, Warsaw University, Banacha 2, 02097, Warsaw, POLAND ABSTRACT We present a model of contextual alignment of biological sequences. It is an extension of the classical alignment, in which we assume that the cost of a substitution depends on the surrounding symbols. In this model the cost of transforming one sequence into another depends on the order of editing operations. We present efficient algorithms for calculating this cost, as well as reconstructing (the representation of) all the orders of operations which yield this optimal cost. A precise characterization of the families of linear orders which can emerge this way is given.
for contextual alignment Substitution Matrices for Contextual Alignment Gambin¡
"... It has been observed that the role an amino acid plays at a site in a protein depends on its environment. To approximate and take advantage of this dependence of context for improving the sensitivity of alignments we propose in [4] a new model for comparison of biological sequences. In this paper we ..."
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It has been observed that the role an amino acid plays at a site in a protein depends on its environment. To approximate and take advantage of this dependence of context for improving the sensitivity of alignments we propose in [4] a new model for comparison of biological sequences. In this paper we present a computational procedure to construct substitution matrices for contextual alignment model. Our method is a suitable adoption of approach of Henikoff & Henikoff [6] to construct a BLOSUM substitution matrix. The drawbacks of the proposed algorithm are discussed. Using this procedure, a number of contextual matrices are generated and some preliminary experiments testing theirs applicability are performed. Motivation There are numerous known examples in biology, showing that indeed context affects the likelihood of changes in amino acids or DNA sequences. One of them is the elimination of adjacent pairs cytosineguanine in DNA, caused by biochemical mechanisms of replication. Another one is observed in proteins: the relevance of the amino acid properties depends on their context. Each amino acid chain occurs in some local environment. These contextual factors have a significant influence on the rates of substitution between the amino acids. For example, the acceptability of various amino acids at a site has been observed to correlate with the polarity of contacting chemical group [8, 10, 12].
Pages S116–S127 Contextual alignment of biological sequences (Extended abstract)
, 2002
"... We present a model of contextual alignment of biological sequences. It is an extension of the classical alignment, in which we assume that the cost of a substitution depends on the surrounding symbols. In this model the cost of transforming one sequence into another depends on the order of editing o ..."
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We present a model of contextual alignment of biological sequences. It is an extension of the classical alignment, in which we assume that the cost of a substitution depends on the surrounding symbols. In this model the cost of transforming one sequence into another depends on the order of editing operations. We present efficient algorithms for calculating this cost, as well as reconstructing (the representation of) all the orders of operations which yield this optimal cost. A precise characterization of the families of linear orders which can emerge this way is given. Contact:
Multiple Sequence Alignment Based on Set Covers
, 2004
"... We introduce a new heuristic for the multiple alignment of a set of sequences. The heuristic is based on a set cover of the residue alphabet of the sequences, and also on the determination of a significant set of blocks comprising subsequences of the sequences to be aligned. These blocks are obtaine ..."
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We introduce a new heuristic for the multiple alignment of a set of sequences. The heuristic is based on a set cover of the residue alphabet of the sequences, and also on the determination of a significant set of blocks comprising subsequences of the sequences to be aligned. These blocks are obtained with the aid of a new data structure, called a suffixset tree, which is constructed from the input sequences with the guidance of the residuealphabet set cover and generalizes the wellknown suffix tree of the sequence set. We provide performance results on selected BAliBASE aminoacid sequences and compare them with those yielded by some prominent approaches.
A Methodology for Determining AminoAcid Substitution Matrices from Set Covers
, 2005
"... We introduce a new methodology for the determination of aminoacid substitution matrices for use in the alignment of proteins. The new methodology is based on a preexisting set cover on the set of residues and on the undirected graph that describes residue exchangeability given the set cover. For fi ..."
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We introduce a new methodology for the determination of aminoacid substitution matrices for use in the alignment of proteins. The new methodology is based on a preexisting set cover on the set of residues and on the undirected graph that describes residue exchangeability given the set cover. For fixed functional forms indicating how to obtain edge weights from the set cover and, after that, substitutionmatrix elements from weighted distances on the graph, the resulting substitution matrix can be checked for performance against some known set of reference alignments and for given gap costs. Finding the appropriate functional forms and gap costs can then be formulated as an optimization problem that seeks to maximize the performance of the substitution matrix on the reference alignment set. We give computational results on the BAliBASE suite using a genetic algorithm for optimization. Our results indicate that it is possible to obtain substitution matrices whose performance is either comparable to or surpasses that of several others, depending on the particular scenario under consideration.