منابع مشابه
De Bruijn Graph Homomorphisms and Recursive De Bruijn Sequences
This paper presents a method to find new de Bruijn cycles based on ones of lesser order. This is done by mapping a de Bruijn cycle to several vertex disjoint cycles in a de Bruijn digraph of higher order and connecting these cycles into one full cycle. We characterize homomorphisms between de Bruijn digraphs of different orders that allow this construction. These maps generalize the well-known ...
متن کاملSparseAssembler: de novo Assembly with the Sparse de Bruijn Graph
de Bruijn graph-based algorithms are one of the two most widely used approaches for de novo genome assembly. A major limitation of this approach is the large computational memory space requirement to construct the de Bruijn graph, which scales with k-mer length and total diversity (N) of unique k-mers in the genome expressed in base pairs or roughly (2k+8)N bits. This limitation is particularly...
متن کاملIdentifying Codes on Directed De Bruijn Graphs
For a directed graph G, a t-identifying code is a subset S ⊆ V (G) with the property that for each vertex v ∈ V (G) the set of vertices of S reachable from v by a directed path of length at most t is both non-empty and unique. A graph is called t-identifiable if there exists a t-identifying code. This paper shows that the de Bruijn graph ~ B(d, n) is 1and 2-identifiable and examines conditions ...
متن کاملMemory Efficient De Bruijn Graph Construction
Massively parallel DNA sequencing technologies are revolutionizing genomics research. Billions of short reads generated at low costs can be assembled for reconstructing the whole genomes. Unfortunately, the large memory footprint of the existing de novo assembly algorithms makes it challenging to get the assembly done for higher eukaryotes like mammals. In this work, we investigate the memory i...
متن کاملA Self-stabilizing General De Bruijn Graph
Searching for other participants is one of the most important operations in a distributed system. We are interested in topologies in which it is possible to route a packet in a fixed number of hops until it arrives at its destination. Given a constant d, this paper introduces a new self-stabilizing protocol for the q-ary d-dimensional de Bruijn graph (q = d √ n) that is able to route any search...
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ژورنال
عنوان ژورنال: Discrete Mathematics
سال: 2009
ISSN: 0012-365X
DOI: 10.1016/j.disc.2007.11.003