Sequence alignment
Image correlation method for DNA sequence alignment.
... New alignment approaches have incorporated digital signal processing ...novel sequence alignment method based on 2-dimensional images, where each nucleic acid base is represented as a fixed gray ...
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Improving transmission efficiency of large sequence alignment/map (SAM) files.
... for sequence alignment data in SAM (Sequence Alignment/Map) format, which improves the compression ratio of existing compression tools ...
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Measuring global credibility with application to local sequence alignment.
... including sequence alignment, RNA structure prediction, phylogenetic inference, motif finding, prediction of pathways, and model selection problems in statistical ...Because sequence alignment ...
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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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AliClu - Temporal sequence alignment for clustering longitudinal clinical data
... The pipeline of the proposed method, which is named the AliClu, is illustrated in Fig. 1. In the first step, the com- plete raw data are pre-processed to obtain the temporal sequences. Then, in the second step, pairwise ...
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Bayesian Top-Down Protein Sequence Alignment with Inferred Position-Specific Gap Penalties.
... 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, Clustal-Ω and ...
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A Parallel Multiobjective Metaheuristic for Multiple Sequence Alignment
... In this paper, we propose the use of Multiobjective Optimization and Evo- lutionary Computation in order to optimize simultaneously quality and con- sistency of the final alignment. We have already applied these ...
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Sequence alignment reveals possible MAPK docking motifs on HIV proteins.
... HIV Sequence Database ...multiple sequence alignments of HIV proteins, and Table 2 shows the percentages of HIV subtype sequences with docking site ...
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SDT: a virus classification tool based on pairwise sequence alignment and identity calculation.
... pairwise sequence identities computed based on multiple sequence alignments rather than on multiple independent pairwise alignments can lead to the deflation of identity scores with increasing dataset ...
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Cloning, structural modelling and characterization of VesT2s, a wasp venom hyaluronidase (HAase) from Vespa tropica
... 4 Sequence alignment of the deduced amino acid sequence of Vespa tropica HAase with other allergen venom ...yellow alignment corresponds to conserved residues in ...acid sequence ...
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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.
... Figure 5. Comparison of YxeF NMR structure (PDB ID 2JOZ, coded in blue) and Blc X-ray crystal structure (PDB ID 3MBT, orange). (A) Structure-based sequence alignment between YxeF and Blc obtained with the ...
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Phylogenetic and temporal dynamics of human immunodeficiency virus type 1 CRF01_AE in China.
... 3. Sequence Alignment and Phylogenetic Tree Analysis The 408 local CRF01_AE gag sequences were aligned with 10 HIV-1 CRF01_AE reference sequences isolated from Thailand, Vietnam, Cyprus, Japan and Hong Kong ...
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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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Exploring fungal diversity: Passalora, Pseudocercospora, Sirosporium and Zasmidium on Brazilian plants
... Abstract Although the genus Pseudocercospora has a worldwide distribution, it is especially diverse in tropical and subtropical countries. Species of this genus are associated with a wide range of plant species, ...
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Diversity of Marine-Derived Fungal Cultures Exposed by DNA Barcodes: The Algorithm Matters.
... multiple sequence alignment algorithm and evolutionary distance estimator in automatic OTU identification via ABGD was ...namely sequence alignment and genetic distance evaluation, are ...
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Expressed Sequence Tags and Gene Prediction
... of sequence alignment programs from National Center for Biotechnology Information (NCBI) that uses the same heuristic approach to identify the best local alignments between the input query and sequences in ...
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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 generations ...
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Menthol binding and inhibition of α7-nicotinic acetylcholine receptors.
... the sequence alignment is not visible in ...high sequence homology between the muscle and the a7- nACh receptor, at these sites, these findings are applicable to possible menthol interactions with ...
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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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Lepidopteran HMG-CoA reductase is a potential selective target for pest control
... using sequence alignment and structural comparison. Sequence analysis showed that the Lepidoptera differ from other ...low sequence identity value compared with ...
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