J. Hein. A new method that simultaneously aligns and reconstructs ancestral sequences for any number of homologous sequences, when the phylogeny is given. Molecular Biology and Evolution, 6:649--668, 1989.  Home/Search   Document Not in Database   Summary   Related Articles   Check

....represent the evolutionary history of a collection of n organisms (or taxa) from their molecular sequence data, or from other form of dissimilarity information. An accurate estimation of this evolutionary history is a very useful tool in many areas of Biology, such as multiple sequence alignment [4], or molecular epidemiological studies of viruses [11] among others. The Phylogeny Problem can then be formulated as finding the phylogenetic tree that best under a certain optimality criterion represents the evolutionary history of a collection of taxa. Unfortunately, this constitutes a very ....

J. Hein. A new method that simultaneously aligns and reconstructs ancestral sequences for any number of homologous sequences, when the phylogeny is given. Molecular Biology and Evolution, 6:649--668, 1989.

....associated sequences. It also plays an important role in determining similar, highly conserved regions across di erent sequences, that might not be so obvious when comparing only two sequences at each time. For di erent algorithms on Multiple Sequence Alignment refer to [CWC92] AL89] CL88] [Hei89] and [Gus97] One of the more commonly used approaches to solving the multiple alignment problem is the tree alignment approach. The ancestral relationship between k given sequences is generally depicted as a phylogenetic tree or as a phylogeny. A phylogenetic tree is the hypothetical ....

J.J. Hein. A new method that simultaneously aligns and reconstructs ancestral sequences for any number of homologous sequences, when the phylogeny is given. Mol.Biol. Evol, 6(6):649-668, 1989.

....of many sequences or their alignments. Meidanis et al. 22] have used directed graphs to represent many similar sequence alignments. We employ the data structure of a sequence graph to represent the image of a cluster. Sequence graphs can efficiently represent large sets of sequences. Hein [13] has introduced sequence graphs to generate a tree alignment. Given two sequence graphs, all sequences on all shortest paths between the represented sequence sets can be efficiently calculated and be represented by a new sequence graph. Some Basic Definitions. We consider sequences a 1 a 2 : ....

....the optimal alignment of two directed networks. Directed networks represent sequences with node labels instead of edge labels. Given two networks N 1 and N 2 representing sequence sets I 1 and I 2 , their algorithm calculates d(I 1 ; I 2 ) for linear gap penalty functions g(k) b Delta k. Hein [13] has rephrased this approach for sequence graphs, in combination with the reasoning of Gotoh [10] in order to handle affine linear gap penalty functions g(k) a b Delta k and represent all sequences on any shortest path between I 1 and I 2 in a new sequence graph. For the purpose of exposition, ....

[Article contains additional citation context not shown here]

J. Hein. A new method that simultaneously aligns and reconstructs ancestral sequences for any number of homologous sequences, when the phylogeny is given. Molecular Biology and Evolution 6:649--668, 1989.

....: s k (i) X (p;q)2E (s p (i) s q (i) 1) The tree score for A is the total scores of all columns in A. It is known that the two definitions of tree alignment are equivalent. Tree alignment was proved to be NP hard [20] Many heuristic algorithms have been proposed in the literature [1, 6, 15, 16]. Some approximation algorithms with guaranteed relative error bounds have been reported recently. In particular, a polynomial time approximation scheme (PTAS) is presented in [21] and improved versions are given in [22, 23] Multigene families, viruses, and alleles from within populations ....

J. Hein, A new method that simultaneously aligns and reconstructs ancestral sequences for any number of homologous sequences, when the phylogeny is given, Mol. Biol. Evol. 6 (1989), 649-668.

....in the space of all sequences. For two sequences, the most parsimonious solutions are all shortest paths between them. Our heuristic uses the sequences on shortest paths between pairs to form the set of candidate ancestral sequences of the two sequences. Sequence graphs, introduced by Hein [4] to generate a tree alignment, efficiently support operations on shortest paths. Given two sequence graphs, all sequences on all shortest paths between the represented sequence sets can be efficiently calculated and be represented by a new sequence graph. We consider sequences a 1 a 2 : an ....

....the optimal alignment of two directed networks. Directed networks represent sequences with node labels instead of edge labels. Given two networks N 1 and N 2 representing sequence sets I 1 and I 2 , their algorithm calculates d(I 1 ; I 2 ) for linear gap penalty functions g(k) b Delta k. Hein [4] has rephrased this approach for sequence graphs, in combination with the reasoning of Gotoh [3] in order to handle affine linear gap penalty functions g(k) a b Delta k and represent all sequences on any shortest path between I 1 and I 2 in a new sequence graph. For the purpose of exposition, ....

[Article contains additional citation context not shown here]

J. Hein. A new method that simultaneously aligns and reconstructs ancestral sequences for any number of homologous sequences, when the phylogeny is given. Molecular Biology and Evolution 6:649--668, 1989.

....6 Experimental results We have implemented DPH Av and DPH F2 in C , using the LEDA library for efficient data structures and algorithms (Mehlhorn and Naher 1995) We compare the results of our algorithms to the latest publicly available version of J. Hein s Treealign (Hein 1989a; Hein 1989b; Hein 1990). We evaluated Treealign on the basis of its tree output, e.g. we calculated the tree length from the multiple alignment that Treealign delivers. Run times of our program range from 20 seconds to 3 minutes on a Sun UltraSparc machine. 6.1 Sample Run for 22 5S rRNA Sequences We evaluated the ....

....than in the case of integer penalties for DNA, and restricting oneself to optimal alignments only allows for a small amount of variation that a sequence graph can express. Suboptimal alignments may shorten the global tree length since more candidates can be offered for Steiner tree construction. Hein (1990) has provided an example where connecting two sequences s 1 and s 2 must miss any optimal tree for s 1 , s 2 and s 3 when the connecting path between s 1 and s 2 is a shortest path obtained from an optimal alignment. Only a slightly suboptimal alignment would leave optimality possible. We are ....

Hein, J. 1989a. A new method that simultaneously aligns and reconstructs ancestral sequences for any number of homologous sequences, when the phylogeny is given. Molecular Biology and Evolution 6, 649--668.

....of many sequences or their alignments. Meidanis et al. 22] have used directed graphs to represent many similar sequence alignments. We employ the data structure of a sequence graph to represent the image of a cluster. Sequence graphs can efficiently represent large sets of sequences. Hein [13] has introduced sequence graphs to generate a tree alignment. Given two sequence graphs, all sequences on all shortest paths between the represented sequence sets can be efficiently calculated and be represented by a new sequence graph. Some basic definitions We consider sequences a 1 a 2 : a ....

....the optimal alignment of two directed networks. Directed networks represent sequences with node labels instead of edge labels. Given two networks N 1 and N 2 representing sequence sets I 1 and I 2 , their algorithm calculates d(I 1 ; I 2 ) for linear gap penalty functions g(k) b Delta k. Hein [13] has rephrased this approach for sequence graphs, in combination with the reasoning of Gotoh [10] in order to handle affine linear gap penalty functions g(k) a b Delta k and represent all sequences on any shortest path between I 1 and I 2 in a new sequence graph. For the purpose of ....

[Article contains additional citation context not shown here]

J. Hein. A new method that simultaneously aligns and reconstructs ancestral sequences for any number of homologous sequences, when the phylogeny is given. Molecular Biology and Evolution 6:649--668, 1989.

....of the Candidate Heuristic, a worst case error bound of 4 d 1 d Gamma1 when the topology is a regular d ary tree. This is made possible by recruiting the candidate sets in lines 4 5 from a limited set of optimal midpoints of certain subsets of the input sequences. Algorithm of Hein. Hein [18, 19] proposes, for the metric case, a version of Candidate Heuristic that is similar to the one of Fitch [5] with two major differences. The first difference is an extension relative to the Fitch algorithm, because Hein does not assume a predefined alignment among the sequences. The second difference ....

....perform is a minimization or maximization, one convertible into the other by negating signs. In this paper we assume a minimization framework, keeping in mind that maximization schemes can be accommodated after trivial modification. Previous methods that use the subtree score to select candidates [18, 21, 20] construct candidate sequences by considering letters from optimal pairwise alignments of two descendant sequences. This procedure only finds all optimal candidates when the mutation score function w satisfies min Gamma w(x; x) w(z; z) Delta w(x; z) w(x; y) w(y; z) for all x; z 2 ....

[Article contains additional citation context not shown here]

J. Hein, A new method that simultaneously aligns and reconstructs ancestral sequences for any number of homologous sequences, when the phylogeny is given, Mol. Biol. Evol., 6 (1989), 649--668.

....the sequences and thus also a set of Steiner points. Unlike in Euclidean space, in sequence space there can be many different shortest paths. One requires a data structure to represent all resulting Steiner sequences. At this point, we employ the concept of a Sequence Graph introduced by Hein [7]. A sequence graph is a network (DAG) with edges annotated by letters or gaps. A sequence that is spelled by letters on the edges of a path from the source to the sink node of the network is said to be represented by the sequence graph. C A C C A T Sequence graph representing the ....

....said to be represented by the sequence graph. C A C C A T Sequence graph representing the sequence set fCA; CC; CT; ACC; ACTg Sequence graphs can represent the Steiner points on all shortest paths between two given sequences (although there may be an exponential number of them) Hein [7] has given a dynamic programming algorithm that calculates a sequence graph representing all shortest paths between two sequences. Furthermore sequence graphs can be aligned thus producing the set of Steiner points between any two closest sequences from the sequence graphs. The algorithm works ....

[Article contains additional citation context not shown here]

J. Hein. A new method that simultaneously aligns and reconstructs ancestral sequences for any number of homologous sequences, when the phylogeny is given. Molecular Biology and Evolution, 6:649--668, 1989.

....to a node by the spanning tree algorithm Foulds et al. instead look for a sequence that lies in between the two species and introduce a new node there. In the world of phylogeny alignment the construction that is closest to coalescement is the use of sequence graphs as introduced by Hein [18]. A sequence graph is a compact structure representing all optimal alignments between two sequences or between two sequence graphs. Formally, a sequence graph is a network (a DAG) with edges annotated by sets of letters or gaps. The sequence graph is constructed in such a way that each path from ....

J. Hein. A new method that simultaneously aligns and reconstructs ancestral sequences for any number of homologous sequences, when the phylogeny is given. Molecular Biology and Evolution, 6:649--668, 1989.

....to a node by the spanning tree algorithm Foulds et al. instead look for a sequence that lies in between the two species and introduce a new node there. In the world of phylogeny alignment the construction that is closest to coalescement is the use of sequence graphs as introduced by Hein [16]. A sequence graph is a compact structure representing all optimal alignments between two sequences or between two sequence graphs. A sequence graph is a network (a DAG) with edges annotated by sets of letters or gaps. The sequence graph is constructed in such a way that each path from the source ....

J. Hein. A new method that simultaneously aligns and reconstructs ancestral sequences for any number of homologous sequences, when the phylogeny is given. Molecular Biology and Evolution, 6:649--668, 1989.

.... [1] Sankoff, Cedergren and Lapalme gave an iterative improvement method to speed up the computation [63, 64] Waterman and Perlwitz devised a heuristic method when the sequences are related by a binary tree [80] Hein proposed a heuristic method based on the concept of a sequence graph [32, 33]. Ravi and Kececioglu designed an approximation algorithm with performance ratio deg 1 deg Gamma1 when the given tree is a regular deg ary tree (i.e. each internal node has exactly deg children) 59] The first approximation algorithm with a guaranteed performance ratio was devised by Wang, ....

J. Hein. A new method that simultaneously aligns and reconstructs ancestral sequences for any number of homologous sequences, when the phylogeny is given, Mol. Biol. Evol., 6 (1989), pp. 649-668.

....but rather only a good enough one, so that it suffices to indicate the correct topology. We direct the interested reader to the following papers which discuss the multiple sequence alignment problem and present results about the computational complexity of the multiple sequence alignment problem [33, 52, 51, 53, 50, 27]. 8.2 Confidence in the output tree If we apply the Witness Antiwitness Method (WAM) to a given set of sequences, we may succeed in recovering the tree correctly, or we may reconstruct a tree different from the true tree, or we may not return any tree at all (i.e. the algorithm may return ....

J. Hein, A new method that simultaneously aligns and reconstructs ancestral sequences for any number of homologous sequences, when the phylogeny is given, Mol. Biol. Evol. 6(1989), 649--668.

No context found.

J. Hein, A new method that simultaneously aligns and reconstructs ancestral sequences for any number of homologous sequences, when the phylogeny is given, Mol. Biol. Evol. 6 (1989) 649 -- 668.

No context found.

J. Hein, A new method that simultaneously aligns and reconstructs ancestral sequences for any number of homologous sequences, when the phylogeny is given, Mol. Biol. Evol. 6(6):649-668m 1989.

No context found.

Hein, J. "A new method that simultaneously aligns and reconstructs ancestral sequences for any number of homologous sequences, when the phylogeny is given." Molecular Biology and Evolution 6:6, 649--668, 1989.

Online articles have much greater impact   More about CiteSeer.IST   Add search form to your site   Submit documents   Feedback  

CiteSeer.IST - Copyright Penn State and NEC