G.H. Gonnet, C. Korostensky, and S. Benner. Evaluation measures of multiple sequence alignments. J Comput Biol., 7(1-2):261--276, 2000.  Home/Search   Document Details and Download   Summary   Related Articles   Check

....is, from leaf A to B, from B to C, from C to D, from D to E and then back from E to leaf A (Figure 2) all edges are counted exactly twice. A circular order is the shortest possible tour through a tree where each leaf is visited once (shortest means smallest sum of edge lengths) see Figure 2) [15]. 2.3 Scoring an Evolutionary Tree Since traversing a tree T (S) in circular order counts each edge in the tree exactly twice, we can derive a function for determining the score of an evolutionary tree using this order. First, we reorder the sequences in S according to the circular order C(S) ....

....# C(S) 2.4 Finding a circular order Since we want to construct an evolutionary tree and therefore do not have any tree, the problem we consider is to find such an order without having any information about the tree structure. But we know that a circular order is the shortest tour through a tree [15]. To solve this problem we reduce it to the symmetric Traveling Salesman Problem (TSP) given is a matrix M that contains the # n 2 # distances of n cities [24, 23] The problem is to find the shortest tour where each city is visited once. We use a modified version of the problem: in our ....

[Article contains additional citation context not shown here]

Gaston H. Gonnet and Chantal Korostensky. Evaluation measures of multiple sequence alignments. J. Comp. Biol., 1999. submitted.

....abstract we present an algorithm that runs in O(n 2 k 2 ) time and produces an MSA whose score is at least n 1 n opt. The score of the alignment represents the probability of the entire evolutionary configuration. In the following sections we briefly explain the scoring function. See [11] for a more detailed exposition. We then describe the algorithm for the calculation of MSAs and present experimental results. 2. Methods 2.0.7. Sum of Pairs versus Circular Sum measure Definition 2.1 The tree T (S) V, E, L) is a binary, leaf labeled tree with leafset L = s 1 , s n ....

....2. Traversal of trees using the SP measure. Some edges are traversed more often than others. exactly twice, independent of the tree structure. A circular order is the shortest possible tour through a tree where each leaf is visited once (shortest means smallest sum of edge lengths) see Figure 3) [11]. Since we do not want to rely on any tree, the problem we consider is to find such an order without having any information about the tree structure. To solve this problem we reduce it to the symmetric Traveling Salesman Problem (TSP) given is a matrix M that contains the # n 2 # distances ....

[Article contains additional citation context not shown here]

G. H. Gonnet and C. Korostensky. Evaluation measures of multiple sequence alignments. J. Comp. Biol., 1999. submitted.

....construction algorithms (Neighbour joining (Saitou and Nei, 1987) clustering methods (Hillis et al. 1996) amongst others) least squares fits to tree topologies, and local optimization routines. There are now routines for tree construction based on circular orders, a new method developed in (Gonnet and Korostensky, 1999). Multiple sequence alignments (Gonnet and Benner, 1996) are created relative to a phylogenetic tree and the system includes several methods for scoring the quality of the alignment including a novel method developed in (Gonnet and Korostensky, 1999) Statistics and Visualization This system ....

.... on circular orders, a new method developed in (Gonnet and Korostensky, 1999) Multiple sequence alignments (Gonnet and Benner, 1996) are created relative to a phylogenetic tree and the system includes several methods for scoring the quality of the alignment including a novel method developed in (Gonnet and Korostensky, 1999). Statistics and Visualization This system includes routines for drawing histograms, dot plots, and bar graphs. The system can also draw unrooted trees, rooted trees, split trees, and combinatorial graphs. There are a large number of routines for producing random permutations, combinations, ....

Gonnet, G. H. and Korostensky, C. (1999) Evaluation measures of multiple sequence alignments. Submitted: J. of Comp. Biochem., 1999.

....from D to E and then back from E to leaf A (Figure 4) all edges are counted exactly twice, independent of the tree structure. A circular order is the shortest possible tour through a tree where each leaf is visited once (shortest in this context means smallest sum of edge lengths) see Figure 4) [15]. Figure 4: Traversal of a tree in circular order 3.3 Scoring an Evolutionary Tree Since traversing a tree T (S) in circular order counts each edge in the tree exactly twice, we can derive a function for determining the score of an evolutionary tree using this order. First, we reorder the ....

....) # C(S) 3.4 Finding a circular order Since we want to construct an evolutionary tree and therefore do not have any tree, the problem we consider is to find such an order without having any information about the tree structure. We know that a circular order is the shortest tour through a tree [15]. To solve this problem we reduce it to the symmetric Traveling Salesman Problem (TSP) given is a matrix M that contains the # n 2 # distances of n cities [24, 23] The problem is to find the shortest tour where each city is visited once. We use a modified version of 1 Note that this score ....

[Article contains additional citation context not shown here]

Gaston H. Gonnet and Chantal Korostensky. Evaluation measures of multiple sequence alignments. J. Comp. Biol., 1999. submitted.

....starts from scratch, but uses the expertise that has evolved over the years. We present a set of heuristics that take as input an MSA that was produced from any algorithm and produces an improved MSA. The scoring of the resulting alignment is based on a probabilistic model that we developed [16]. With this scoring function we can determine the upper bound (maximum possible score) so we know when the MSA is optimal. The heuristics use the fact that if the sequences in the MSA are related, there exists an (unknown) evolutionary tree. It treats gaps as a special character as gaps play a ....

....function F(A) of an MSA is similar to the sum of pairs measure [4] except that we do not add all scores of all pairwise alignments, but only the scores of the pairwise alignments in the TSP order C(S) divided by two. A TSP order is a circular order with respect to the associated evolutionary tree [16]. Problem 1.2 (TSP problem) Given is a set of sequences S = s 1 , s n and the corresponding scores of the optimal pairwise alignments. The problem is to find the longest tour where each sequence is visited once. Definition 1.7 The TSP order C(S) of set of sequences S = s 1 , s ....

[Article contains additional citation context not shown here]

Gaston H. Gonnet and Chantal Korostensky. Evaluation measures of multiple sequence alignments. J. Comp. Biol., 1999. submitted.

....multiple alignment. It is easy to verify the accuracy, as we know the correct alignment by construction. The comparisons were done for this and several other algorithms available to us. These results and the description of the methodology exceed the scope of the paper and will be available in [9]. One problem affects the quality of these multiple alignments. The results are dependent on a correct EPT, which is not always available. Minor errors in the EPT are of little consequence, unless they straddle incorrectly a point where an indel occurred. This causes the same indel to be in ....

Gaston H. Gonnet and Chantal Korostensky. Evaluation measures of multiple sequence alignments. In preparation, 1996.

No context found.

G.H. Gonnet, C. Korostensky, and S. Benner. Evaluation measures of multiple sequence alignments. J Comput Biol., 7(1-2):261--276, 2000.

No context found.

G.H. Gonnet, C. Korostensky, and S. Benner. Evaluation measures of multiple sequence alignments. J Comput Biol., 7(1-2):261--276, 2000.

No context found.

G.H. Gonnet, C. Korostensky, and S. Benner. Evaluation measures of multiple sequence alignments. J Comput Biol., 7(1-2):261--276, 2000.

No context found.

G.H. Gonnet, C. Korostensky, and S. Benner. Evaluation measures of multiple sequence alignments. J Comput Biol., 7(1-2):261--276, 2000.

No context found.

Gonnet, G.H., C. Korostensky, and S. Benner, Evaluation measures of multiple sequence alignments. J Comput Biol, 2000. 7(1-2): p. 261-76.

No context found.

Gonnet GH, Korostensky C, Benner S. Evaluation measures of multiple sequence alignments. J Comput Biol 2000;7(1-2):261-76.

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