de Bruijn sequences
Binary De Bruijn sequences for DS CDMA systems: analysis and results
... binary De Bruijn sequences, avoiding the need to exhaustively evaluate the cross-correlation values in a given family may be very important, due to the computational burden associated to the huge ...
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Uniformly de Bruijn sequences and symbolic Diophantine approximation on fractals
... infinite de Bruijn sequences in order to answer closely related ...infinite de Bruijn sequences in k ≥ 2 letters, thought of as a set of real numbers via a decimal expansion, has ...
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Uniformly de Bruijn sequences and symbolic Diophantine approximation on fractals
... infinite de Bruijn sequences in order to answer closely related ...infinite de Bruijn sequences in k ≥ 2 letters, thought of as a set of real numbers via a decimal expansion, has ...
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De Bruijn Sequences from Joining Cycles of Nonlinear Feedback Shift Registers
... De Bruijn sequences are a class of nonlinear recurring sequences that have wide appli- cations in cryptography and modern communication ...of de Bruijn sequences are ...
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On cross joining de Bruijn sequences
... modified de Bruijn sequences of order n = ...the sequences generated by them has seven cross-join ...modified de Bruijn ...
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De Bruijn Sequences from Symmetric Shift Registers
... just one n-stage scattered symmetric FSR, and it requires no more than 2n comparisons and n + 1 FSR shifts to generate the next state in the full cycle from the current state. By further analyse the cycle structure of ...
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State of the art de novoassembly of human genomes from massively parallel sequencing data
... 10 de Bruijn graphs were introduced to compact potential over- laps by shared k-mers (vertex in the graph) among reads, to reduce the intense read comparison com- ...
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Accuracy of Different Bioinformatics Methods in Detecting Antibiotic Resistance and Virulence Factors from Staphylococcus aureus Whole Genome Sequences
... Velvet de novo assemblies: other newer assemblers ...long-read sequences will require further software testing, although Mykrobe has been successfully used for initial resistance calling in Mycobacterium ...
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Using cascading Bloom filters to improve the memory usage for de Brujin graphs
... A de Bruijn graph, for a given parameter k, of a set of reads (strings) R ⊆ ∗ = { A, C, T, G } ∗ is entirely defined by the set T ⊆ U = k of k-mers present in ...its de Bruijn graph using a ...
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Jabba: hybrid error correction for long sequencing reads
... Recently, third generation sequencing technologies (Pacific Biosciences, 2013; Oxford Nano Technolo- gies, 2014) began to emerge. Pacific Biosciences SMRT sequencing results in much longer reads (avg. >5000 ...
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Development of a laser pointer mouse
... The speed of interaction with the interactive white boards would vary based on their de- sign. The Nintendo Wii adaptation although the cheapest upgrade (Lee 2008, Wikipedia 2010c), would be the slowest and less ...
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Fast read alignment with incorporation of known genomic variants
... Local and global alignments play a fundamental role in HTS read mapping and downstream sequence analysis, i.e., the CIGAR outcome of the alignment contributes to variant calling and structural variation detection. How- ...
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Konnector v2.0: pseudo-long reads from paired-end sequencing data
... represent de Bruijn graphs, as demonstrated by the Minia assembler ...filter de Bruijn graphs, false positives manifest themselves as false branches, as depicted by the yellow nodes in Figure ...
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Dense edge disjoint embedding of complete binary trees in interconnection networks
... hypercube, de Bruijn and shue-exchange graphs our embeddings show that the complete binary tree can be embedded with disjoint edges in hosts that are generally half the size compared with previously ...
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Bloom Filter Trie: an alignment-free and reference-free data structure for pan-genome storage
... labeled de Bruijn graph with it requires concatenated raw sequence files as input, where it is not possible to specify a minimum number of occurences per ...
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Hematopoietic stem cell emergence in the conceptus and the role of Runx1
... cis-acting sequences neces- sary to drive the full spectrum of Runx1 expression at this ...acting sequences sufficient for runx1 expression in the dorsal aorta are contained within 8 kb upstream of the P2 ...
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A novel codon based de Bruijn graph algorithm for gene construction from unassembled transcriptomes
... Because some true ORFs are discarded during SVM fil- tration, a codon-based de Bruijn graph constructed from rORFs alone may result in fragmented CDSs. To solve this problem, we generated a more complete ...
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Space-efficient and exact de Bruijn graph representation based on a Bloom filter
... The de Bruijn graph of a set of DNA or RNA sequences is a data structure which plays an increasingly impor- tant role in next-generation sequencing ...perform de novo assembly of DNA ...
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A representation of a compressed de Bruijn graph for pan-genome analysis that enables search
... of this paper is a new space-efficient representation of the compressed de Bruijn graph that can be calculated with A4 . This new representation adds the possibility to search for a pattern (e.g. an ...
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Evaluation of PCR for Diagnosis of American Cutaneous Leishmaniasis in an Area of Endemicity in Northeastern Brazil
... tations, the clinical evolution and response to chemotherapy may differ for ACL caused by the two subgenera (24). Thus, approaches allowing the discrimination between the New World dermotropic leishmanias (subgenus ...
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