Efficient Bubble Enumeration in Directed Graphs

Abstract : 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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String Processing and Information Retrieval (SPIRE), Oct 2012, Cartagena, Colombia. 7608, pp.118-129, 2012, Lecture Notes in Computer Science. <10.1007/978-3-642-34109-0_13>


https://hal.inria.fr/hal-00738927
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Submitted on : Friday, October 5, 2012 - 1:54:03 PM
Last modification on : Tuesday, June 30, 2015 - 1:26:40 PM

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Etienne 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. 7608, pp.118-129, 2012, Lecture Notes in Computer Science. <10.1007/978-3-642-34109-0_13>. <hal-00738927>

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