DNA sequence alignment with mosaic structure
DNA Sequence Alignment Analysis
... (vi) Test for recombination in the X-linked genes — is there evidence for recombination? The X sequences yield a minimum number of recombination events, Rm = 6 (and Y gives zero). The X don't fit zero recombination. I ...
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DNA Sequence alignment using programme by algorithm
... Miropeats alignment diagrams but they have their own particular ...single sequence. A sequence can be plotted against itself and regions that share ...
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Improving Short DNA Sequence Alignment with Parallel Computing
... It was ex- pected that multithreaded BWA would outperform parallel BWA for the suffix array index generation stage when BWA was run with the same number of threads as par[r] ...
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An Exact Nonparametric Method for Inferring Mosaic Structure in Sequence Triplets
... detecting mosaic structure or recombination among nucleotide sequences usually rely on identifying a pattern or a signal that would be unlikely to appear under clonal ...the mosaic-producing ...the ...
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Multiple sequence alignment algorithms for the phylogenic analysis of chloroplast DNA
... 2. Sequence Alignment 2. Sequence Alignment 2.1 Introduction Approximate string matching has been an important tool in computational biology since small variations within DNA or protein ...
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DNA Sequence Alignment Algorithm Based on k tuple Statistics
... Therefore, the frequency of loop statements in line 9 and line 10 can be regarded as a constant. Accordingly, the time complexity of SDkS is O(n), where n=max(L 1 , L 2 ). Experiments and Results In this section, SHR ...
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Design and implementation of FPGA based DNA sequence alignment accelerator
... query sequence with 32 characters is forwarded into the systolic array that means each processing unit holds a character from the query ...subject sequence drove into the systolic array by each internal ...
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Local DNA sequence alignment in a cluster of workstations: Algorithms and tools
... 6. Conclusion and Future Work In this paper, we proposed and evaluated one parallel and distributed approach to solve the DNA local and global sequence alignment problem. A DSM system was chosen ...
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Hadoop Performance Analysis on Raspberry Pi for DNA Sequence Alignment
... to DNA sequence and amino acids. Next-generation DNA sequencing are generating billions of sequence data; it's made sequence alignment cannot perform on standalone ...for ...
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Prediction Of Antimicrobial Peptides Based On Sequence Alignment And Secondary Structure Sequence And Segment Sequence.pdf
... secondary structure sequence from the prediction of ...including sequence alignment stage and feature extraction process until classification stage is carried out in Perl programming language ...
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Accelerating pairwise DNA Sequence Alignment using the CUDA compatible GPU
... each DNA nucleotide in the two sequences and fill the initialization vector at the GPU with values for both DNA nucleotide match and ...first sequence nucleotide and second sequence nucleotide ...
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iPBA: a tool for protein structure comparison using sequence alignment strategies.: Structural Alphabet Alignment
... accurate structure com- parison has been ...for structure comparison, based on a struc- tural ...3D structure can be translated into a 1D sequence of ...improved alignment approach ...
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Pairwise Sequence Alignment
... the sequence is completely palindromic in the displayed ...palindromic sequence (For DNA sequences this refers to a perfect match of the normal strand with its reverse complement, which is frequently ...
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Sequence and structure alignment of paramyxovirus hemagglutinin-neuraminidase with influenza virus neuraminidase.
... Site- directed mutagenesis of the neuraminidase active site sug- gests that the enzyme activity is very sensitive to single amino acid sequence changes in both the functional and framewo[r] ...
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An Exact Mathematical Programming Approach to Multiple RNA Sequence-Structure Alignment
... We want to show that our model yields on aver- age comparable or better alignments than other state- of-the-art programs that build upon more costly dy- namic programming algorithms. We do believe that this comparison is ...
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An Exact Mathematical Programming Approach to Multiple RNA Sequence-Structure Alignment
... We want to show that our model yields on aver- age comparable or better alignments than other state- of-the-art programs that build upon more costly dy- namic programming algorithms. We do believe that this comparison is ...
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Mosaic DNA imports with interspersions of recipient sequence after natural transformation of Helicobacter pylori
... exogenous DNA, and recombination during mixed infections of one stomach with multiple ...donor DNA were interrupted by short interspersed sequences of the recipient (ISR) with a mean length of 82 ...
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Genome sequence analysis of DNA A from okra yellow vein mosaic virus isolates
... of DNA-A using begomovirus component equivalent to DNA-A in diseased bhendi ...a DNA-A and β-DNA component from BYVMV infected bhendi tissue, which together with BYVMV, causes typical yellow ...
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Accurate multiple sequence-structure alignment of RNA sequences using combinatorial optimization
... Comparison of running times. We compared the programs tested on the same computing server with an Intel Xeon CPU running at 3.2 GHz, 3.5 GB RAM, and Linux kernel version 2.6.16. It turned out that memory requirement was ...
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Accurate multiple sequence-structure alignment of RNA sequences using combinatorial optimization
... the structure they are forming, because their evolutionary behavior fol- lows the structure-function paradigm: RNA molecules with different sequences but same or similar secondary struc- ture are likely to ...
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