Results 41 to 50 of about 1,513,801 (381)
On the Complexity of Multiple Sequence Alignment [PDF]
Journal of Computational Biology, 1994 We study the computational complexity of two popular problems in multiple sequence alignment: multiple alignment with SP-score and multiple tree alignment. It is shown that the first problem is NP-complete and the second is MAX SNP-hard. The complexity of tree alignment with a given phylogeny is also considered.
Tao Jiang, Lusheng Wang
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Enhanced Genetic Method for Optimizing Multiple Sequence Alignment
Mathematics, 2023 In the realm of bioinformatics, Multiple Sequence Alignment (MSA) is a pivotal technique used to optimize the alignment of multiple biological sequences, guided by specific scoring criteria.
Mohammed K. Ibrahim +3 more
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MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability
Molecular biology and evolution, 2013 We report a major update of the MAFFT multiple sequence alignment program. This version has several new features, including options for adding unaligned sequences into an existing alignment, adjustment of direction in nucleotide alignment, constrained ...
K. Katoh, D. Standley
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Bootstrapping Lexical Choice via Multiple-Sequence Alignment [PDF]
, 2002 An important component of any generation system is the mapping dictionary, a lexicon of elementary semantic expressions and corresponding natural language realizations.
Barzilay, Regina, Lee, Lillian
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A benchmark study of sequence alignment methods for protein clustering
BMC Bioinformatics, 2018 Background Protein sequence alignment analyses have become a crucial step for many bioinformatics studies during the past decades. Multiple sequence alignment (MSA) and pair-wise sequence alignment (PSA) are two major approaches in sequence alignment ...
Yingying Wang, Hongyan Wu, Yunpeng Cai
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Nucleic Acids Research, 1997 CLUSTAL X is a new windows interface for the widely-used progressive multiple sequence alignment program CLUSTAL W. The new system is easy to use, providing an integrated system for performing multiple sequence and profile alignments and analysing the ...
J. Thompson +4 more
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Nucleic Acids Research, 1994 The sensitivity of the commonly used progressive multiple sequence alignment method has been greatly improved for the alignment of divergent protein sequences.
J. Thompson, D. Higgins, T. Gibson
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Lower bounds on multiple sequence alignment using exact 3-way alignment
BMC Bioinformatics, 2007 Background Multiple sequence alignment is fundamental. Exponential growth in computation time appears to be inevitable when an optimal alignment is required for many sequences. Exact costs of optimum alignments are therefore rarely computed. Consequently
Colbourn Charles J, Kumar Sudhir
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MUSCLE: multiple sequence alignment with high accuracy and high throughput.
Nucleic Acids Research, 2004 We describe MUSCLE, a new computer program for creating multiple alignments of protein sequences. Elements of the algorithm include fast distance estimation using kmer counting, progressive alignment using a new profile function we call the log ...
Robert C. Edgar
semanticscholar +1 more source
Multiple sequence alignments in linguistics [PDF]
Proceedings of the EACL 2009 Workshop on Language Technology and Resources for Cultural Heritage, Social Sciences, Humanities, and Education - LaTeCH-SHELT&R '09, 2009 In this study we apply and evaluate an iterative pairwise alignment program for producing multiple sequence alignments, ALPHAMALIG (Alonso et al., 2004), using as material the phonetic transcriptions of words used in Bulgarian dialectological research. To evaluate the quality of the multiple alignment, we propose two new methods based on comparing each
Martijn Wieling +2 more
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