Clustal W multiple sequence alignment: Evolutionary conservation of
Solving multiple sequence alignment problems using various evolutionary algorithm
... In case of quality improvement, the alteration is accepted and the working set is stored in the list of "best temporary solutions.” [7] Otherwise, the new alignment is discarded. The proposed approach below ...
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Heuristics for multiobjective multiple sequence alignment
... We analysed the effect of different k-values in the k-block neighborhood, as well as the effect of the three starting alignments on the performance of PLS. For a given instance, let Min denote the length of the smallest ...
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A Tabu Search Approach to Multiple Sequence Alignment
... an alignment (with a negative cost) and rewards matches between base pairs (with a positive ...to sequence alignment, the simplest way that a sequence can evolve would be through a minimal ...
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Multiple Sequence Alignment by Conformational Space Annealing
... INTRODUCTION Multiple sequence alignment (MSA) is a fundamental prob- lem in computational biology and bioinformatics, where ei- ther related proteins from the same organism or similar proteins from ...
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Progressive Multiple Sequence Alignment with Indel Evolution
... PIP evolutionary model, we have developed and implemented – for the first time in the frequentist framework – a progressive MSA algorithm with an explicit evolutionary model of substitutions, insertions and ...
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Cluster Analysis Method for Multiple Sequence Alignment
... of sequence alignment. The problem of multiple sequence alignment (MSA) is a proposition of evolutionary ...individual sequence position is established for each column in ...
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Instability in progressive multiple sequence alignment algorithms
... real alignment scores using an amino acid weight matrix such as BLOSUM [7], the number of possible scores is still finite although much greater than with k-tuple ...such alignment scores is limited how- ...
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Assessing the efficiency of multiple sequence alignment programs
... between alignment accuracy and computational cost has become a critical indicator of the most suitable MSA ...CLUSTALW, CLUSTAL OMEGA, DIALIGN-TX, MAFFT, MUSCLE, POA, Probalign, Probcons and T-Coffee, ...
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Progressive multiple sequence alignment with indel evolution
... explicit evolutionary model of substitu- tions, insertions and ...the alignment of two MSAs by ML, which exploits PIP’s linear time complexity for the computation of marginal likeli- ...particular ...
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Memory-Efficient A* Heuristics for Multiple Sequence Alignment
... In multiple sequence alignment, three or more se- quences must be aligned, so even with Hirschberg-style one- dimensional space reductions, DP algorithms still require too much ...the ...
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Viewing multiple sequence alignments with the JavaScript Sequence Alignment Viewer (JSAV)
... first sequence alignment viewer and editor implemented in Java, a platform independent programming language allowing graphical user interfaces (GUIs) to run on any operating ...ClustalW multiple ...
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Viewing multiple sequence alignments with the JavaScript Sequence Alignment Viewer (JSAV)
... Viewing multiple sequence alignments (MSAs) is a fundamental requirement in the analysis of protein sequences, allowing us to visu- alize conservation across protein families as well as unusual ...
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Multiple Sequence Alignment and Analysis: Part I An Introduction to the Theory and Application of Multiple Sequence Analysis.
... ‘more similar’ than others! 4. Similarity and Significance. People are often confused by the distinction between homology and similarity: There is a huge difference! Similarity is merely a statistical parameter that ...
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Multiple sequence alignment with user-defined anchor points
... different alignment algorithms. Thus, alignment programs can be evaluated by their abil- ity to correctly align these core ...various alignment situations, ...full-length sequence sets ...
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Integer Linear Programming Models for Multiple Sequence Alignment
... Introduction Multiple sequence alignment (MSA) is a pop- ular research area in bioinformatics that con- sists in arranging more than two biological se- quences, usually DNA, RNA, or protein se- ...
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Progressive multiple sequence alignment with the Poisson Indel Process
... Abstract Sequence alignment lies at the heart of many evolutionary and com- parative genomics ...optimal alignment of multiple sequences is NP-hard, so that exact algorithms become ...
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Multiple sequence alignment augmented by expert user constraints
... a sequence with other characters over ...DNA sequence alignments, where the similarity between sequences depends on their time since divergence and the substitution rates as represented in the ...
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Multiple sequence alignment with user-defined constraints at GOBICS
... to multiple sequence alignment in which the user can explicitly specify parts of the sequences that are biologically related to each ...a multiple alignment that respects these ...
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Multiple sequence alignment algorithms for the phylogenic analysis of chloroplast DNA
... 2. Sequence Alignment 2. Sequence Alignment ...and/or evolutionary relationships between the sequences (Baxevanis & Ouellette ...
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Inferring phylogenies of evolving sequences without multiple sequence alignment
... key evolutionary processes remain to be ...simulated sequence sets of various sizes in both nucleotides and amino acids, we systematically assess the accuracy of phylogenetic inference using an ...
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