An efficient search algorithm to find the elementary circuits of a graph
Communications of the ACM
De novo repeat classification and fragment assembly
RECOMB '04 Proceedings of the eighth annual international conference on Resaerch in computational molecular biology
Identifying SNPs without a reference genome by comparing raw reads
SPIRE'10 Proceedings of the 17th international conference on String processing and information retrieval
Discrete Applied Mathematics
| Hi-index | 0.00 |
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.