An \bm -Time Algorithm for Detecting Superbubbles
In genome assembly graphs, motifs such as tips, bubbles, and cross links are studied in order to find sequencing errors and to understand the nature of the genome. Superbubble, a complex generalization of bubbles, was recently proposed as an important subgraph class for analyzing assembly graphs. At...
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| Veröffentlicht in: | IEEE/ACM transactions on computational biology and bioinformatics 2015-07, Vol.12 (4), p.770-777 |
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| container_title | IEEE/ACM transactions on computational biology and bioinformatics |
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| creator | Wing-Kin Sung Sadakane, Kunihiko Shibuya, Tetsuo Belorkar, Abha Pyrogova, Iana |
| description | In genome assembly graphs, motifs such as tips, bubbles, and cross links are studied in order to find sequencing errors and to understand the nature of the genome. Superbubble, a complex generalization of bubbles, was recently proposed as an important subgraph class for analyzing assembly graphs. At present, a quadratic time algorithm is known. This paper gives an O(m log m)-time algorithm to solve this problem for a graph with m edges. |
| doi_str_mv | 10.1109/TCBB.2014.2385696 |
| format | Article |
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| source | IEEE Electronic Library (IEL) |
| subjects | Algorithms Assembly Bioinformatics Biology Bubbles Computational biology Genome assembly Genomes Genomics Graph theory Graphs Merging Next generation sequencing Sequential analysis Superbubble |
| title | An \bm -Time Algorithm for Detecting Superbubbles |
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