Local multiple sequence alignment using dead-end elimination
نویسندگان
چکیده
منابع مشابه
Optimization Alignment: the End of Multiple Sequence Alignment in Phylogenetics?
A method is described to assess directly the number of DNA sequence transformations, evolutionary events, required by a phylogenetic topology without the use of multiple sequence alignment. This is accomplished through a generalization of existing character optimization procedures to include insertion and deletion events (indels) in addition to base substitutions. The crux of the model is the t...
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Sequence alignment is an important task in bioinformatics which involves typical database search where data is in the form of DNA, RNA or protein sequence. For alignment various methods have been devised starting from pairwise alignment to multiple sequence alignment (MSA). To perform multiple sequence alignment various methods exists like progressive, iterative and concepts of dynamic programm...
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Soft neighborhood substitutability (SNS) is a powerful technique to automatically detect and prune dominated solutions in combinatorial optimization. Recently, it has been shown in [26] that enforcing partial SNS (PSNS) during search can be worthwhile in the context of Weighted Constraint Satisfaction Problems (WCSP). However, for some problems, especially with large domains, PSNS is still too ...
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MOTIVATION Dead-End Elimination (DEE) is a powerful algorithm capable of reducing the search space for structure-based protein design by a combinatorial factor. By using a fixed backbone template, a rotamer library, and a potential energy function, DEE identifies and prunes rotamer choices that are provably not part of the Global Minimum Energy Conformation (GMEC), effectively eliminating the m...
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ژورنال
عنوان ژورنال: Bioinformatics
سال: 1999
ISSN: 1367-4803,1460-2059
DOI: 10.1093/bioinformatics/15.11.947