Results 1  10
of
46
A General Edit Distance between RNA Structures
, 2001
"... Arcannotated sequences are useful in representing the structural information of RNA sequences. ..."
Abstract

Cited by 71 (0 self)
 Add to MetaCart
Arcannotated sequences are useful in representing the structural information of RNA sequences.
The Longest Common Subsequence Problem for ArcAnnotated Sequences
 In Proc. of 11th CPM, number 1848 in LNCS
, 2000
"... . Arcannotated sequences are useful in representing the structural information of RNA and protein sequences. Recently, the longest arcpreserving common subsequence problem has been introduced in [6, 7] as a framework for studying the similarity of arcannotated sequences. In this paper, we con ..."
Abstract

Cited by 35 (1 self)
 Add to MetaCart
. Arcannotated sequences are useful in representing the structural information of RNA and protein sequences. Recently, the longest arcpreserving common subsequence problem has been introduced in [6, 7] as a framework for studying the similarity of arcannotated sequences. In this paper, we consider arcannotated sequences with various arc structures and present some new algorithmic and complexity results on the longest arcpreserving common subsequence problem. Some of our results answer an open question in [6, 7] and some others improve the hardness results in [6, 7]. Keywords: sequence annotation, longest common subsequence, approximation algorithm, maximum independent set, MAX SNPhard, dynamic programming. 1
Computing the Similarity of Two Sequences with Nested Arc Annotations
 Theoretical Computer Science
, 2003
"... We present exact algorithms for the NPcomplete Longest Common Subsequence problem for sequences with nested arc annotations, a problem occurring in structure comparison of RNA. Given two sequences of length at most n and nested arc structure, one of our algorithms determines (if existent) in O(3.3 ..."
Abstract

Cited by 20 (2 self)
 Add to MetaCart
We present exact algorithms for the NPcomplete Longest Common Subsequence problem for sequences with nested arc annotations, a problem occurring in structure comparison of RNA. Given two sequences of length at most n and nested arc structure, one of our algorithms determines (if existent) in O(3.31 time an arcpreserving subsequence of both sequences, which can be obtained by deleting (together with corresponding arcs) k 1 letters from the first and k 2 letters from the second sequence. A second algorithm shows that (in case of a four letter alphabet) we can find a length l arcannotated subsequence in O(12 n) time. This means that the problem is fixedparameter tractable when parameterized by the number of deletions as well as when parameterized by the subsequence length. Our findings complement known approximation results which give a quadratic time factor2approximation for the general and polynomial time approximation schemes for restricted versions of the problem. In addition, we obtain further fixedparameter tractability results for these restricted versions.
Alignment of Protein Structures with a Memetic Evolutionary Algorithm
 In GECCO2002: Proceedings of the Genetic and Evolutionary Computation Conference
, 2002
"... CATEGORY: RealWorld Applications Structural comparison of proteins is a core problem in modern biomedical research. ..."
Abstract

Cited by 19 (10 self)
 Add to MetaCart
CATEGORY: RealWorld Applications Structural comparison of proteins is a core problem in modern biomedical research.
Cliquedetection Models in Computational Biochemistry and Genomics
 European Journal of Operational Research
, 2005
"... Many important problems arising in computational biochemistry and genomics have been formulated in terms of underlying combinatorial optimization models. In particular, a number have been formulated as cliquedetection models. The proposed article includes an introduction to the underlying biochemis ..."
Abstract

Cited by 17 (1 self)
 Add to MetaCart
Many important problems arising in computational biochemistry and genomics have been formulated in terms of underlying combinatorial optimization models. In particular, a number have been formulated as cliquedetection models. The proposed article includes an introduction to the underlying biochemistry and genomic aspects of the problems as well as to the graphtheoretic aspects of the solution approaches. Each subsequent section describes a particular type of problem, gives an example to show how the graph model can be derived, summarizes recent progress, and discusses challenges associated with solving the associated graphtheoretic models. Clique detection models include prescribing (a) a maximal clique, (b) a maximum clique, (c) a maximum weighted clique, or (d) all maximal cliques in a graph. The particular types of biochemistry and genomics problems that can be represented by a clique detection model include integration of genome mapping data, nonoverlapping local alignments, matching and comparing molecular structures, and protein docking.
Matt: local flexibility aids protein multiple structure alignment
 PLoS Comput. Biol
, 2008
"... Even when there is agreement on what measure a protein multiple structure alignment should be optimizing, finding the optimal alignment is computationally prohibitive. One approach used by many previous methods is aligned fragment pair chaining, where short structural fragments from all the proteins ..."
Abstract

Cited by 15 (1 self)
 Add to MetaCart
Even when there is agreement on what measure a protein multiple structure alignment should be optimizing, finding the optimal alignment is computationally prohibitive. One approach used by many previous methods is aligned fragment pair chaining, where short structural fragments from all the proteins are aligned against each other optimally, and the final alignment chains these together in geometrically consistent ways. Ye and Godzik have recently suggested that adding geometric flexibility may help better model protein structures in a variety of contexts. We introduce the program Matt (Multiple Alignment with Translations and Twists), an aligned fragment pair chaining algorithm that, in intermediate steps, allows local flexibility between fragments: small translations and rotations are temporarily allowed to bring sets of aligned fragments closer, even if they are physically impossible under rigid body transformations. After a dynamic programming assembly guided by these ‘‘bent’ ’ alignments, geometric consistency is restored in the final step before the alignment is output. Matt is tested against other recent multiple protein structure alignment programs on the popular Homstrad and SABmark benchmark datasets. Matt’s global performance is competitive with the other programs on Homstrad, but outperforms the other programs on SABmark, a benchmark of multiple structure alignments of proteins with more distant homology. On both datasets, Matt demonstrates an ability to better align the ends of ahelices and bstrands, an important characteristic of any structure alignment program intended to help construct a structural template library for threading approaches to the inverse proteinfolding
Self Generating Metaheuristics in Bioinformatics: The Proteins Structure Comparison Case
 Genetic Programming and Evolvable Machines
, 2004
"... In this paper we describe the application of a so called "SelfGenerating" Memetic Algorithm to the Maximum Contact Map Overlap problem (MAXCMO). The maximum overlap of contact maps is emerging as a leading modeling technique to obtain structural alignment among pairs of protein structures. Identif ..."
Abstract

Cited by 15 (5 self)
 Add to MetaCart
In this paper we describe the application of a so called "SelfGenerating" Memetic Algorithm to the Maximum Contact Map Overlap problem (MAXCMO). The maximum overlap of contact maps is emerging as a leading modeling technique to obtain structural alignment among pairs of protein structures. Identifying structural alignments (and hence similarity among proteins) is essential to the correct assessment of the relation between proteins structure and function. A robust methodology for structural comparison could have impact on the process of rational drug design.
Opportunities for Combinatorial Optimization In Computational Biology
, 2003
"... This is a survey designed for mathematical programming people who do not know molecular biology and want to learn the kinds of combinatorial optimization problems that arise. After a brief introduction to the biology, we present optimization models pertaining to sequencing, evolutionary explanations ..."
Abstract

Cited by 14 (0 self)
 Add to MetaCart
This is a survey designed for mathematical programming people who do not know molecular biology and want to learn the kinds of combinatorial optimization problems that arise. After a brief introduction to the biology, we present optimization models pertaining to sequencing, evolutionary explanations, structure prediction and recognition. Additional biology is given in the context of the problems, including some motivation for disease diagnosis and drug discovery. Open problems are cited with an extensive bibliography, and we o er a guide to getting started in this exciting frontier.
Towards Optimally Solving the Longest Common Subsequence Problem for Sequences with Nested Arc Annotations in Linear Time
 In Proc. of the 13th Symposium on Combinatorial Pattern Matching (CPM02), volume 2373 of LNCS
, 2002
"... We present exact algorithms for the NPcomplete Longest Common Subsequence problem for sequences with nested arc annotations, a problem occurring in structure comparison of RNA. Given two sequences of length at most n and nested arc structure, our algorithm determines (if existent) in time O(3.3 ..."
Abstract

Cited by 14 (1 self)
 Add to MetaCart
We present exact algorithms for the NPcomplete Longest Common Subsequence problem for sequences with nested arc annotations, a problem occurring in structure comparison of RNA. Given two sequences of length at most n and nested arc structure, our algorithm determines (if existent) in time O(3.31 k 1 +k 2 n) an arcpreserving subsequence of both sequences, which can be obtained by deleting (together with corresponding arcs) k1 letters from the first and k2 letters from the second sequence. Thus, the problem is fixedparameter tractable when parameterized by the number of deletions. This complements known approximation results which give a quadratic time factor2approximation for the general and polynomial time approximation schemes for restricted versions of the problem. In addition, we obtain further fixedparameter tractability results for these restricted versions.
Approximating the 2interval pattern problem
 IN PROCEEDINGS OF THE 13TH ANNUAL EUROPEAN SYMPOSIUM ON ALGORITHMS (ESA
, 2005
"... We address the problem of approximating the 2Interval Pattern problem over its various models and restrictions. This problem, which is motivated by RNA secondary structure prediction, asks to find a maximum cardinality subset of a 2interval set with respect to some prespecified model. For each s ..."
Abstract

Cited by 14 (6 self)
 Add to MetaCart
We address the problem of approximating the 2Interval Pattern problem over its various models and restrictions. This problem, which is motivated by RNA secondary structure prediction, asks to find a maximum cardinality subset of a 2interval set with respect to some prespecified model. For each such model, we give varying approximation quality depending on the different possible restrictions imposed on the input 2interval set.