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Weyer-Menkhoff J: Multiple sequence alignment with user-defined constraints at GOBICS
- Bioinformatics
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Cited by 39 (11 self)
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This is an Open Access article distributed under the terms of the Creative Commons Attribution License
Aligning Alignments
- In 9-th Annual Symp. Combinatorial Pattern Matching, Volume 1448 of LNCS
, 1998
"... While the area of sequence comparison has a rich collection of results on the alignment of two sequences, and even the alignment of multiple sequences, there is little known about the alignment of two alignments. The problem becomes interesting when the alignment objective function counts gaps, as i ..."
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Cited by 18 (2 self)
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While the area of sequence comparison has a rich collection of results on the alignment of two sequences, and even the alignment of multiple sequences, there is little known about the alignment of two alignments. The problem becomes interesting when the alignment objective function counts gaps, as is common when aligning biological sequences, and has the form of the sum-of-pairs objective. We begin a thorough investigation of aligning two alignments under the sum-of-pairs objective with general linear gap costs when either of the two alignments are given in the form of a sequence (a degenerate alignment containing a single sequence) , a multiple alignment (containing two or more sequences), or a profile (a representation of a multiple alignment often used in computational biology). This leads to five problem variations, some of which arise in widely-used heuristics for multiple sequence alignment, and in assessing the relatedness of a sequence to a sequence family. For variations in w...
Near Optimal Multiple Alignment Within a Band In Polynomial Time
- In Proc. of 32nd ACM STOC
, 2000
"... Multiple sequence alignment is one of the most important problems in computational biology. Because of its notorious difficulties, aligning sequences within a constant band is a popular practice in bioinformatics with good results [17; 13; 14; 15; 1; 3; 6; 20; 18]. However, the problem is still NP-h ..."
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Cited by 10 (0 self)
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Multiple sequence alignment is one of the most important problems in computational biology. Because of its notorious difficulties, aligning sequences within a constant band is a popular practice in bioinformatics with good results [17; 13; 14; 15; 1; 3; 6; 20; 18]. However, the problem is still NP-hard for multiple sequences. In this paper, we present polynomial time approximation schemes (PTAS) for multiple sequence alignment within a constant band, under standard models of SP alignment and consensus (star) alignment. The algorithms work for very general score schemes. In order to prove our main results, we also present a PTAS for SP alignment and a PTAS for consensus alignment, allowing only constant number of insertion and deletion gaps (of arbitrary length) per sequence on the average. 1.
Consistent Equivalence Relations: a Set-Theoretical Framework for Multiple Sequence Alignment
, 1999
"... Recently, Morgenstern et al. have proposed a new mathematical definition of sequence alignment (Morgenstern et al.,1996). In this paper, we discuss this definition in more detail. We demonstrate that it provides an appropriate conceptual framework in which problems arising in the context of sequ ..."
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Cited by 6 (0 self)
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Recently, Morgenstern et al. have proposed a new mathematical definition of sequence alignment (Morgenstern et al.,1996). In this paper, we discuss this definition in more detail. We demonstrate that it provides an appropriate conceptual framework in which problems arising in the context of sequence alignment can be treated systematically. 1 1 Introduction In the standard theory of sequence alignment, an alignment of N sequences s 1 ; : : : ; s N is defined as a matrix, whose rows are so-called `padded sequences' s 1 ; : : : ; s N , which are obtained from the original sequences by insertion of additional characters designated as `blanks', `gap characters' or `neutral elements' (cf. Waterman, 1995; p. 186). This formal definition corresponds to the way alignments are constructed by standard alignment algorithms: Following a method developed in 1970 by Needleman and Wunsch (Needleman & Wunsch, 1970), alignments are constructed by inserting gaps into sequences (and by penalizi...
RE-MuSiC: a tool for multiple sequence alignment with regular expression constraints
, 2007
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Efficient Sequence Alignment with Side-Constraints by Cluster Tree Elimination
"... Aligning DNA and protein sequences is a core technique in molecular biology. Often, it is desirable to include partial prior knowledge and conditions in an alignment. Going beyond prior work, we aim at the integration of such side constraints in free combination into alignment algorithms. The most c ..."
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Aligning DNA and protein sequences is a core technique in molecular biology. Often, it is desirable to include partial prior knowledge and conditions in an alignment. Going beyond prior work, we aim at the integration of such side constraints in free combination into alignment algorithms. The most common and successful technique for efficient alignment algorithms is dynamic programming (DP). However, a weakness of DP is that one cannot include additional constraints without specifically tailoring a new DP algorithm. Here, we discuss a declarative approach that is based on constraint techniques and show how it can be extended by formulating additional knowledge as constraints. We take special care to obtain the efficiency of DP for sequence alignment. This is achieved by careful modeling and applying proper solving strategies. Finally, we apply our method to the scanning for RNA motifs in large sequences. This case study demonstrates how the new approach can be used in real biological problems. A prototypic implementation of the method is available at
Experimenting with the MetaFork framework targeting multicores
, 2013
"... The work reported in this report evaluates the correctness, performance and usefulness of the four MetaFork translators (MetaFork to CilkPlus, CilkPlus to MetaFork, MetaFork to OpenMP, OpenMP to MetaFork). To this end, we run these translates on various input programs written either in CilkPlus or O ..."
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The work reported in this report evaluates the correctness, performance and usefulness of the four MetaFork translators (MetaFork to CilkPlus, CilkPlus to MetaFork, MetaFork to OpenMP, OpenMP to MetaFork). To this end, we run these translates on various input programs written either in CilkPlus or OpenMP, or both.
ral ssBioMed CentAlgorithms for Molecular Biology Open AcceResearch Multiple sequence alignment with user-defined anchor points
"... Background: Automated software tools for multiple alignment often fail to produce biologically meaningful results. In such situations, expert knowledge can help to improve the quality of alignments. Results: Herein, we describe a semi-automatic version of the alignment program DIALIGN that can take ..."
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Background: Automated software tools for multiple alignment often fail to produce biologically meaningful results. In such situations, expert knowledge can help to improve the quality of alignments. Results: Herein, we describe a semi-automatic version of the alignment program DIALIGN that can take pre-defined constraints into account. It is possible for the user to specify parts of the sequences that are assumed to be homologous and should therefore be aligned to each other. Our software program can use these sites as anchor points by creating a multiple alignment respecting these constraints. This way, our alignment method can produce alignments that are biologically more meaningful than alignments produced by fully automated procedures. As a demonstration of how our method works, we apply our approach to genomic sequences around the Hox gene cluster and to a set of DNA-binding proteins. As a by-product, we obtain insights about the performance of the greedy algorithm that our program uses for multiple alignment and about the underlying objective function. This information will be useful for the further development of DIALIGN. The described alignment approach has been integrated into the TRACKER software system.
unknown title
, 2007
"... constraint reduces the size of the space that a dynamic programming implementation must search for an optimal pairwise alignment. Some algorithms, such as T-Coffee (Notredame et al., 2000) and DbClustal (Thompson et al., 2000), do use libraries of pairwise alignments, but they do not attempt to expl ..."
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constraint reduces the size of the space that a dynamic programming implementation must search for an optimal pairwise alignment. Some algorithms, such as T-Coffee (Notredame et al., 2000) and DbClustal (Thompson et al., 2000), do use libraries of pairwise alignments, but they do not attempt to explicitly choose alignments present in multiple pairs. 3. An easy way for users to specify regions they want to see aligned in any multiple alignment computed. User input can be particularly useful when user knowledge is not reflected in sequence similarity. Such a capability was added to a semiautomatic version of DIALIGN (Morgenstern et al., 1998) by Morgenstern et al. (2006). Other methods (for example SALIGN in MODELLER (Marti-Renom et al., 2004)) include the option for a user to specify constraints when aligning sequences and structures.
