[PDF] Top 20 On cross joining de Bruijn sequences
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On cross joining de Bruijn sequences
... arbitrary de Bruijn sequence could be obtained by applying cross-join pair operations to a given ...generating de Bruijn sequences starting from a given ...modified de ... See full document
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Binary De Bruijn sequences for DS CDMA systems: analysis and results
... of sequences that we need to perform our correlation-related evalua- ...the sequences having the same span n must be generated at the same ...the sequences, we introduce in the generation process a ... See full document
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Uniformly de Bruijn sequences and symbolic Diophantine approximation on fractals
... Remark 3.3. If m = n and ω is de Bruijn, then γ is a simple path that visits each vertex exactly once. However, since γ starts and ends at different vertices, it is not a Hamiltonian cycle, contrary to [1, ... See full document
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Jabba: hybrid error correction for long sequencing reads
... Whereas LoRDEC relies on shared k-mers to align the long reads to a de Bruijn graph, we explore the idea of using maximal exact matches (MEMs). MEMs are exact matches between two sequences that can ... See full document
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Vol 7, No 2 (2015)
... the De Bruijn sequences, exhibited even for small values of the span, allows to find a big amount of subsets providing the ZCZ property among the sequences, joint security-related ...5 ... See full document
5
On the representation of gliders in Rule 54 by de Bruijn and cycle diagrams
... De Bruijn diagrams have demonstrated their power in representing periodic strings based in gliders in elemental CA ...these sequences, ...that de Bruijn diagrams grow exponentially, so ... See full document
10
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 ... See full document
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A novel codon based de Bruijn graph algorithm for gene construction from unassembled transcriptomes
... codon-based de Bruijn graph, which contains a con- siderably decreased number of nodes and edges (by approximately 60%) compared with the traditional ...codon-based de Bruijn graph are simple ... See full document
12
Uniformly de Bruijn sequences and symbolic Diophantine approximation on fractals
... Classically, the field of Diophantine approximation sought to quantify how well real numbers can be approximated by rationals, weighing the distance to the rational point against some function of its de- ... See full document
18
De Bruijn Sequences from Joining Cycles of Nonlinear Feedback Shift Registers
... The n-stage FSRs constructed in Corollary 1 generates only short cycles of lengths at most 4n. An example of such FSRs is given in Example 1. These FSRs are good candidates for the cycle joining algorithms ... See full document
31
De Bruijn Sequences from Symmetric Shift Registers
... Constructing De Bruijn sequences by joining the cycles of a nonlinear feedback shift register (NFSR) is a challenging work, because many fundamental problems related to NFSRs are essentially ... See full document
13
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 ... See full document
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State of the art de novoassembly of human genomes from massively parallel sequencing data
... the de Bruijn graph step, neither ABySS nor SOAPdenovo take advan- tage of paired-end information in the initial contig ...original de Bruijn graph could be explained by inadequate overlap ... See full document
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Scaffolder - software for manual genome scaffolding
... The choice of nucleotide sequences comprising the scaf- fold is specified using the YAML syntax [23]. YAML is a data format using whitespace and indentation to pro- duce a machine readable structure. As YAML is a ... See full document
6
Molecular characterisation of alpinia species from western ghats
... The evolutionary history was inferred using the maximum parsimony method 34 . Tree #1 out of 3 most parsimonious trees (length = 55) is shown. The consistency index is 0.981818 (0.923077), the retention index is 0.933333 ... See full document
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Identification of ion channel genes in the Acyrthosiphon pisum genome
... subunit. Interestingly, it does have orthologues of insect subunits shown to be targeted by imidacloprid (Apisuma2) (Matsuda et al., 1998) and spinosad (Apisuma6) (Perry et al., 2007). Also, of considerable interest is ... See full document
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Accuracy of Different Bioinformatics Methods in Detecting Antibiotic Resistance and Virulence Factors from Staphylococcus aureus Whole Genome Sequences
... performs de novo assembly using Velvet v1.0.18 (20). These de novo assemblies formed the basis for the Typewriter program, whereas Genefinder used the raw sequencing ... See full document
12
Direct repeats of the herpes simplex virus a sequence promote nonconservative homologous recombination that is not dependent on XPF/ERCC4.
... Mechanisms for circularization of the HSV genome. Her- pesviruses all have linear genomes of double-stranded DNA that need to be circularized before efficient replication of the viral chromosomes can take place (23). ... See full document
8
Diversity of Microorganisms Isolated from the Soil Sample surround Chroogomphus rutilus in the Beijing Region
... ITS sequences can accumulate muta- tions at a faster rate than the ...gene sequences of the 14 isolates were compared with sequences listed in DDBJ/EMBL/GenBank, indicating that they had significant ... See full document
12
Complete genome sequence of Paenibacillus sp. strain JDR-2
... Pjdr2 was the first member of this genus to have its genome completely sequenced and made available for detailed analysis. The sequences of genomes of 2 strains of Paenibacillus polymyxa [5,6], “ Paenibacillus ... See full document
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