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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.
S. Rezaei, J. Bai
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DNA multiple sequence alignments [PDF]
, 2002 In 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.
Jyrki Muona +2 more
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Multiple Sequence Alignment [PDF]
, 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 with Clustal X
Trends in Biochemical Sciences, 1998The Clustal series of programs are widely used for multiple alignment and for preparing phylogenetic trees. The programs have undergone several incarnations, and 1997 saw the release of the Clustal W 1.7 upgrade and of Clustal X, which has a windows interface.
Jeanmougin, F. +4 more
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Optimization of multiple‐sequence alignment based on multiple‐structure alignment
Proteins: Structure, Function, and Bioinformatics, 2005AbstractRoutinely used multiple‐sequence alignment methods use only sequence information. Consequently, they may produce inaccurate alignments. Multiple‐structure alignment methods, on the other hand, optimize structural alignment by ignoring sequence information.
Maxim Shatsky +3 more
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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.
Jaap Heringa, Michael Sammeth
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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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Multiple Sequence Alignment with DIALIGN
2013DIALIGN is a software tool for multiple sequence alignment by combining global and local alignment features. It composes multiple alignments from local pairwise sequence similarities. This approach is particularly useful to discover conserved functional regions in sequences that share only local homologies but are otherwise unrelated.
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2017
Introduction Phylogeny estimation generally begins by estimating a multiple sequence alignment on the set of sequences. Once the multiple sequence alignment is computed, a tree can then be computed on the alignment (Figure 9.1). Not surprisingly, errors in multiple sequence alignment estimation tend to produce errors in estimated ...
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Introduction Phylogeny estimation generally begins by estimating a multiple sequence alignment on the set of sequences. Once the multiple sequence alignment is computed, a tree can then be computed on the alignment (Figure 9.1). Not surprisingly, errors in multiple sequence alignment estimation tend to produce errors in estimated ...
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Overestimation for Multiple Sequence Alignment
2007 IEEE Symposium on Computational Intelligence and Bioinformatics and Computational Biology, 2007Multiple sequence alignment is an important problem in computational biology. A-star is an algorithm that can be used to find exact alignments. We present a simple modification of the A-star algorithm that improves much multiple sequence alignment, both in time and memory, at the cost of a small accuracy loss.
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