Results 11 to 20 of about 628,105 (211)
Multiple Sequence Alignment Based on Profile Alignment of Intermediate Sequences [PDF]
Journal of Computational Biology, 2007 Despite considerable efforts, it remains difficult to obtain accurate multiple sequence alignments. By using additional hits from database search of the input sequences, a few strategies have been proposed to significantly improve alignment accuracy, including the construction of profiles from the hits while performing profile alignment, the inclusion ...
Yue Lu, Sing-Hoi Sze
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Constrained sequence alignment [PDF]
Bulletin of Mathematical Biology, 1993 This paper presents a dynamic programming algorithm for aligning two sequences when the alignment is constrained to lie between two arbitrary boundary lines in the dynamic programming matrix. For affine gap penalties, the algorithm requires only O(F) computations time and O(M+N) space, when F is the area of the feasible region and M and N are the ...
Chao, Kun-Mao +2 more
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Multiple sequence alignments [PDF]
Current Opinion in Structural Biology, 2005 Multiple sequence alignments are very widely used in all areas of DNA and protein sequence analysis. The main methods that are still in use are based on 'progressive alignment' and date from the mid to late 1980s. Recently, some dramatic improvements have been made to the methodology with respect either to speed and capacity to deal with large numbers ...
Iain M, Wallace +2 more
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Optimal sequence alignments [PDF]
Proceedings of the National Academy of Sciences, 1983 Current theory is adequate to the task of finding an optimal alignment between two character strings such as nucleic acids. Most algorithms currently in use must fail to find the homologous alignment between a set of codons for the chicken α- and β-hemoglobin sequence when it is in fact discoverable by a more general treatment of gaps.
W M, Fitch, T F, Smith
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On the Complexity of Sequence to Graph Alignment [PDF]
Journal of Computational Biology, 2019 Abstract Availability of extensive genetics data across multiple individuals and populations is driving the growing importance of graph based reference representations. Aligning sequences to graphs is a fundamental operation on several types of sequence graphs (variation graphs, assembly graphs, pan-genomes, etc.) and
Jain, Chirag +3 more
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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.
Lusheng Wang 0001, Tao Jiang 0001
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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
Prokić, J., Wieling, M., Nerbonne, J.
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On the number of alignments ofk sequences [PDF]
Graphs and Combinatorics, 1990 zbMATH Open Web Interface contents unavailable due to conflicting licenses.
Hanlon, P. +3 more
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Sequence Alignment as Hypothesis Testing [PDF]
Journal of Computational Biology, 2011 Sequence alignment depends on the scoring function that defines similarity between pairs of letters. For local alignment, the computational algorithm searches for the most similar segments in the sequences according to the scoring function. The choice of this scoring function is important for correctly detecting segments of interest.
Lu Meng +3 more
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Sequence‐to‐sequence alignment using a pendulum
IET Computer Vision, 2015 Analysing two or more video sequences of dynamic scenes typically requires time synchronisation between sequences, where this alignment is not always possible using hardware. A particular method will most likely process the entire, frequently lengthy, imaged material, requiring additional processing which normally serves for synchronisation only ...
Tomislav Pribanic +2 more
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