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Conference Papers Year : 2012

Efficient Bubble Enumeration in Directed Graphs


Polymorphisms in DNA- or RNA-seq data lead to recognisable patterns in a de Bruijn graph representation of the reads obtained by sequencing. such patterns have been called mouths, or bubbles in the literature. They correspond to two vertex-disjoint directed paths between a source $s$ and a target $t$. Due to the high number of such bubbles that may be present in real data, their enumeration is a major issue concerning the efficiency of dedicated algorithms. We propose in this paper the first linear delay algorithm to enumerate all bubbles with a given source.
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hal-00738927 , version 1 (05-10-2012)



Etienne E. Birmelé, Pierluigi Crescenzi, Rui Ferreira, Roberto Grossi, Vincent Lacroix, et al.. Efficient Bubble Enumeration in Directed Graphs. String Processing and Information Retrieval (SPIRE), Oct 2012, Cartagena, Colombia. pp.118-129, ⟨10.1007/978-3-642-34109-0_13⟩. ⟨hal-00738927⟩
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