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Multiple Sequence Alignment: Methods and Protocols
Methods in Molecular Biology, 2021M. Q P I L L L V M L R-L L--M K-I L L L-M P P V L I L
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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 ...
D G, Higgins, W 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 ...
D G, Higgins, W R, Taylor
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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.
D J, Bacon, W 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.
D J, Bacon, W F, Anderson
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T-Coffee: A novel method for fast and accurate multiple sequence alignment.
Journal of Molecular Biology, 2000We describe a new method (T-Coffee) for multiple sequence alignment that provides a dramatic improvement in accuracy with a modest sacrifice in speed as compared to the most commonly used alternatives.
C. Notredame, D. Higgins, J. Heringa
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Multithreaded Multiple Sequence Alignments
2005 IEEE Engineering in Medicine and Biology 27th Annual Conference, 2005Based on the mixed idea of Progressive alignment and Divide-and-conquer alignment, two different multithreaded multiple sequence alignment programs, depending on how the guide tree(s) would be applied, are implemented for checking the improvements of alignment speed and sensitivity.
Joanne, Bai, Siamak, Rezaei
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2016
The increasing importance of Next Generation Sequencing (NGS) techniques has highlighted the key role of multiple sequence alignment (MSA) in comparative structure and function analysis of biological sequences. MSA often leads to fundamental biological insight into sequence-structure-function relationships of nucleotide or protein sequence families ...
Bawono, Punto +5 more
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The increasing importance of Next Generation Sequencing (NGS) techniques has highlighted the key role of multiple sequence alignment (MSA) in comparative structure and function analysis of biological sequences. MSA often leads to fundamental biological insight into sequence-structure-function relationships of nucleotide or protein sequence families ...
Bawono, Punto +5 more
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DNA multiple sequence alignments
2002In this chapter we examine the procedure of multiple sequence alignment. We first examine the heuristic procedures commonly used in multiple sequence alignment. Next we examine sources of ambiguity involved in the alignment procedure. We suggest that several alignment parameters be employed to examine alignment sensitivity.
Gonzalo, Giribet +2 more
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Multiple protein sequence alignment
Current Opinion in Structural Biology, 2008Multiple sequence alignments are essential in computational analysis of protein sequences and structures, with applications in structure modeling, functional site prediction, phylogenetic analysis and sequence database searching. Constructing accurate multiple alignments for divergent protein sequences remains a difficult computational task, and ...
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2015
Multiple Sequence alignment (MSA) is a generalization of Pairwise Sequence Alignment to multiple sequences. Thus, instead of aligning two sequences, the objective in MSA is to align k sequences simultaneously such an overall functional is optimized. The motivation behind doing a MSA is that it allows us to extract consensus evident in a widely diverse ...
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Multiple Sequence alignment (MSA) is a generalization of Pairwise Sequence Alignment to multiple sequences. Thus, instead of aligning two sequences, the objective in MSA is to align k sequences simultaneously such an overall functional is optimized. The motivation behind doing a MSA is that it allows us to extract consensus evident in a widely diverse ...
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Global multiple‐sequence alignment with repeats
Proteins: Structure, Function, and Bioinformatics, 2006AbstractRepeating fragments in biological sequences are often essential for structure and function. Over the years, many methods have been developed to recognize repeats or to multiply align protein sequences. However, the integration of these two methodologies has been largely unexplored to date.
Sammeth, M., Heringa, J.
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