Multiple sequence alignment
A Parallel Multiobjective Metaheuristic for Multiple Sequence Alignment
... The alignment among three or more nucleotides/amino-acids sequences at the same time is known as Multiple Sequence Alignment (MSA), an NP-hard optimization ...timal alignment raises ...
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Diversity of Marine-Derived Fungal Cultures Exposed by DNA Barcodes: The Algorithm Matters.
... Multiple sequence alignment and evolutionary distance estimates Table 1 presents alignment statistics for each of the tested alignment algorithms, performed online under default ...the ...
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Structural insights into leishmanolysins encoded on chromosome 10 of Leishmania (Viannia) braziliensis
... the multiple sequence alignment of the 29 leishmanolysin sequences encoded on chromosome 10, we distinguished subgroups presenting three specific patches of residues along the 62 ...
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DendroBLAST: approximate phylogenetic trees in the absence of multiple sequence alignments.
... simulated multiple sequence alignments. The simulated multiple sequence alignments on which these methods were tested do not contain any alignment induced ...true multiple ...
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Identifying Likely Transmission Pathways within a 10-Year Community Outbreak of Tuberculosis by High-Depth Whole Genome Sequencing.
... reference sequence reduces the potential for sequencing errors and false variant calls, compared with de novo assembly; however, mapping against a reference genome introduces a bias towards the reference ...
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Analysis of genotype diversity and evolution of Dengue virus serotype 2 using complete genomes
... The steps involved in the study of genetic structure of DENV-2 population using population genetics approach include (i) multiple sequence alignment (MSA) of 990 DENV-2 genomes using MUSCLE program ...
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Cl gene cluster encoding several small nucleolar RNAs: a comparison amongst trypanosomatids
... 2: multiple sequence alignment by CLUSTAL W of H/ACA Cl- small nucleolar RNAs (snoRNAs) from different trypanosomatid spe- snoRNAs) from different trypanosomatid spe- ...
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Genetic Algorithm Based Approach for Obtaining Alignment of Multiple Sequences
... Genetic Algorithm with local search optimization embedded on its mutation operators for performing multiple sequence alignment. But its mutation probability leads to better solutions in fewer ...
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Development Of Method To Derive Variation Pattern In Neuraminidase Enzyme Of Influenza-A Virus And Predict The Most Probable Upcoming Subtype.
... The influenza A virus has proven to be lethal over the history of time. Every season the virus is usually formed from a new combination of various subtypes of hemagglutinin and neuraminidase. It is impossible to ...
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Bayesian Top-Down Protein Sequence Alignment with Inferred Position-Specific Gap Penalties.
... protein multiple sequence alignment (MSA) that, as implemented in the program GISMO and applied to large numbers of diverse sequences, is more accurate than the popular MSA programs MUSCLE, MAFFT, ...
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An Efficient Parallel Processing Approach For Multiple Biological Sequence Alignment
... Simultaneous alignments are high quality heuristics that deliver an alignment usually very close to optimality. They nonetheless remain an extremely CPU and memory-intensive approach, applicable only to about nine ...
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Fungi in Thailand: a case study of the efficacy of an ITS barcode for automatically identifying species within the Annulohypoxylon and Hypoxylon genera.
... its sequence using different types of alignment (e.g., local alignment; see Figure S1) and sequence ...a multiple-test ...any multiple-testing correction, so readers can correct ...
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MACSE: Multiple Alignment of Coding SEquences accounting for frameshifts and stop codons.
... each sequence is translated with the same reading frame from beginning to end, so that the presence of a single additional nucleotide leads to both aberrant translation and ...coding sequence ...
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Processing multiple non-adjacent dependencies: evidence from sequence learning
... require keeping track of dependency relations over a rela- tively long distance (see also Hurford [14], for an observation that German students have less difficulties with nested dependencies than English students). The ...
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NMR structure of lipoprotein YxeF from Bacillus subtilis reveals a calycin fold and distant homology with the lipocalin Blc from Escherichia coli.
... As indicated above, the C-terminal domain of a self-compart- mentalizing protease Pab87 from Pyrococcus abyssi has been suggested to be the first domain with lipocalin-like architecture from Archaea [17]. Notably, the ...
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Cloning, structural modelling and characterization of VesT2s, a wasp venom hyaluronidase (HAase) from Vespa tropica
... The basic characterizations of the gene and protein se- quences were analyzed using NCBI (http://www.ncbi.nlm. nih.gov/Database/index.html) and the basic local alignment search tool BLAST ...
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A horizontal alignment tool for numerical trend discovery in sequence data: application to protein hydropathy.
... 70% sequence identity by the cd-hit server [41], resulting in 214 representative ...each sequence were averaged over a window size of 15 residues, with the average being assigned to the middle position of ...
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Paulo Sérgio Schlögl1 , André Luis Wendt dos Santos2 , Leila do Nascimento Vieira1, Eny Iochevet Segal Floh2 and Miguel Pedro Guerra1
... acid sequence identity with not only putative AGO1 homo- logues from Populus trichocarpa (97%), but also with AGO1 and ZLL (ZWILLE) proteins from Arabidopsis (91% and 89%, ...respectively). Sequence ...
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SDT: a virus classification tool based on pairwise sequence alignment and identity calculation.
... pairwise sequence identity scores that are widely used for this ...novel sequence is most closely related to and, depending on the colours of the cells in the matrix, immediately indicates which genus, ...
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Effective identification of conserved pathways in biological networks using hidden Markov models.
... network alignment algorithm that can be used for finding conserved pathways in two or more biological ...proposed alignment algorithm has a number of important advantages compared to other existing local ...
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