An O(m log m)-Time Algorithm for Detecting Superbubbles

IEEE/ACM Trans Comput Biol Bioinform. 2015 Jul-Aug;12(4):770-7. doi: 10.1109/TCBB.2014.2385696.

Abstract

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.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Algorithms*
  • Genomics / methods*
  • High-Throughput Nucleotide Sequencing / methods*
  • Humans
  • Sequence Analysis, DNA / methods*