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Current Opinion in Structural Biology, 2006
Multiple sequence alignments are an essential tool for protein structure and function prediction, phylogeny inference and other common tasks in sequence analysis. Recently developed systems have advanced the state of the art with respect to accuracy, ability to scale to thousands of proteins and flexibility in comparing proteins that do not share the ...
Robert C. Edgar, Serafim Batzoglou
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Multiple sequence alignments are an essential tool for protein structure and function prediction, phylogeny inference and other common tasks in sequence analysis. Recently developed systems have advanced the state of the art with respect to accuracy, ability to scale to thousands of proteins and flexibility in comparing proteins that do not share the ...
Robert C. Edgar, Serafim Batzoglou
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Journal of Molecular Biology, 1986
A method has been developed for aligning segments of several sequences at once. The number of search steps depends only polynomially on the number of sequences, instead of exponentially, because most alignments are rejected without being evaluated explicitly. A data structure herein called the "heap" facilitates this process.
David J. Bacon, Wayne F. Anderson
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A method has been developed for aligning segments of several sequences at once. The number of search steps depends only polynomially on the number of sequences, instead of exponentially, because most alignments are rejected without being evaluated explicitly. A data structure herein called the "heap" facilitates this process.
David J. Bacon, Wayne F. Anderson
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2003
Publisher Summary This chapter discusses various aspects of multiple sequence alignment. Dynamic programming can be generalized to more than two sequences where one finds the multiple alignments with the best score according to the scoring scheme. Gaps are scored according to their length and the number of sequences that they occur in and the method ...
Desmond G. Higgens, William R. Taylor
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Publisher Summary This chapter discusses various aspects of multiple sequence alignment. Dynamic programming can be generalized to more than two sequences where one finds the multiple alignments with the best score according to the scoring scheme. Gaps are scored according to their length and the number of sequences that they occur in and the method ...
Desmond G. Higgens, William R. Taylor
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Aligning a DNA sequence with a protein sequence
Proceedings of the first annual international conference on Computational molecular biology - RECOMB '97, 1997We develop several algorithms for the problem of aligning DNA sequence with a protein sequence. Our methods account for frameshift errors, but not for introns in the DNA sequence. Thus, they are particularly appropriate for comparing a cDNA sequence that suffers from sequencing errors with an amino acid sequence or a protein sequence database.
Zheng Zhang +2 more
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2008
Multiple sequence alignment (MSA) has assumed a key role in comparative structure and function analysis of biological sequences. It often leads to fundamental biological insight into sequence-structure-function relationships of nucleotide or protein sequence families.
Pirovano, W., Heringa, J.
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Multiple sequence alignment (MSA) has assumed a key role in comparative structure and function analysis of biological sequences. It often leads to fundamental biological insight into sequence-structure-function relationships of nucleotide or protein sequence families.
Pirovano, W., Heringa, J.
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Aligning Sequences to Structures
2007Most newly sequenced proteins are likely to adopt a similar structure to one which has already been experimentally determined. For this reason, the most successful approaches to protein structure prediction have been template-based methods. Such prediction methods attempt to identify and model the folds of unknown structures by aligning the target ...
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Bioinformatics, 1994
We present a dynamic programming algorithm for computing a best global alignment of two sequences. The proposed algorithm is robust in identifying any of several global relationships between two sequences. The algorithm delivers a best alignment of two sequences in linear space and quadratic time.
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We present a dynamic programming algorithm for computing a best global alignment of two sequences. The proposed algorithm is robust in identifying any of several global relationships between two sequences. The algorithm delivers a best alignment of two sequences in linear space and quadratic time.
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Consistency of optimal sequence alignments [PDF]
Bulletin of Mathematical Biology, 1990 Pairwise optimal alignments between three or more sequences are not necessarily consistent as a whole, but consistent and inconsistent residues are usually distributed in clusters. An efficient method has been developed for locating consistent regions when each pairwise alignment is given in the form of a "skeletal representation" (Bull. math. Biol. 52,
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2022
This chapter focuses on comparing sequences using alignment. Sequence alignment is the operation that consists of matching two or more sequences, in order to highlight their similarity, whether it is local or global. If the alignment is given, then computing a score is a relatively simple task.
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This chapter focuses on comparing sequences using alignment. Sequence alignment is the operation that consists of matching two or more sequences, in order to highlight their similarity, whether it is local or global. If the alignment is given, then computing a score is a relatively simple task.
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Sequence Alignment with Tandem Duplication
Journal of Computational Biology, 1997Algorithm development for comparing and aligning biological sequences has, until recently, been based on the SI model of mutational events which assumes that modification of sequences proceeds through any of the operations of substitution, insertion or deletion (the latter two collectively termed indels). While this model has worked fairly well, it has
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