Results 41 to 50 of about 3,685 (173)
BMC Bioinformatics, 2020 Background De Bruijn graphs are key data structures for the analysis of next-generation sequencing data. They efficiently represent the overlap between reads and hence, also the underlying genome sequence.
Aranka Steyaert +2 more
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DRAGoM: Classification and Quantification of Noncoding RNA in Metagenomic Data
Frontiers in Genetics, 2021 Noncoding RNAs (ncRNAs) play important regulatory and functional roles in microorganisms, such as regulation of gene expression, signaling, protein synthesis, and RNA processing. Hence, their classification and quantification are central tasks toward the
Ben Liu +6 more
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Bisecting de Bruijn and Kautz graphs
Discrete Applied Mathematics, 1998 zbMATH Open Web Interface contents unavailable due to conflicting licenses.
José D. P. Rolim +3 more
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BMC Genomics, 2019 Background A popular strategy to study alternative splicing in non-model organisms starts from sequencing the entire transcriptome, then assembling the reads by using de novo transcriptome assembly algorithms to obtain predicted transcripts. A similarity
Shuhua Fu +5 more
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Practical dynamic de Bruijn graphs [PDF]
Bioinformatics, 2018 Abstract Motivation The de Bruijn graph is fundamental to the analysis of next generation sequencing data and so, as datasets of DNA reads grow rapidly, it becomes more important to represent de Bruijn graphs compactly while still supporting fast assembly. Previous implementations of compact de Bruijn
Victoria G. Crawford +4 more
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BdBG: a bucket-based method for compressing genome sequencing data with dynamic de Bruijn graphs [PDF]
PeerJ, 2018 Dramatic increases in data produced by next-generation sequencing (NGS) technologies demand data compression tools for saving storage space. However, effective and efficient data compression for genome sequencing data has remained an unresolved challenge
Rongjie Wang +4 more
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Colouring of cycles in the de bruijn graphs
Discussiones Mathematicae Graph Theory, 2000 The authors show that the problem of finding the family of all locally reducible factors in the binary de Bruijn graph of order \(k\) is equivalent to the problem of finding all colourings of the edges in the binary de Bruijn graph of order \(k-1\), where each vertex belongs to exactly two cycles of different colours.
Ewa Lazuka, Jerzy Zurawiecki
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Fully Dynamic de Bruijn Graphs [PDF]
, 2016 We present a space- and time-efficient fully dynamic implementation de Bruijn graphs, which can also support fixed-length jumbled pattern matching.
Djamal Belazzougui +3 more
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, 2012 We propose a new succinct de Bruijn graph representation. If the de Bruijn graph of k-mers in a DNA sequence of length N has m edges, it can be represented in 4m+o(m) bits. This is much smaller than existing ones. The numbers of outgoing and incoming edges of a node are computed in constant time, and the outgoing and incoming edge with given label are ...
Alexander Bowe +3 more
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Making de Bruijn Graphs Eulerian.
, 2022 A directed multigraph is called Eulerian if it has a circuit which uses each edge exactly once. Euler’s theorem tells us that a weakly connected directed multigraph is Eulerian if and only if every node is balanced. Given a collection S of strings over an alphabet Σ, the de Bruijn graph (dBG) of order k of S is a directed multigraph G_{S,k}(V,E), where
G. Bernardini (Giulia) +5 more
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