A biclique approach to reference anchored gene blocks and its applications to pathogenicity Islands

Research output: Chapter in Book/Report/Conference proceedingConference contributionpeer-review


We formalize a new problem variant in gene-block discovery, denoted Reference-Anchored Gene Blocks (RAGB). Given a query sequence Q of length n, representing the gene-array of a DNA element, a window size bound d on the length of a substring of interest in Q, and a set of target gene sequences T = {T1…Tc}. Our objective is to identify gene-blocks in T that are centered in a subset q of co-localized genes from Q, and contain genomes from T in which the corresponding orthologs of the genes from q are also co-localized. We cast RAGB as a variant of a (colored) biclique problem in bipartite graphs, and analyze its parameterized complexity, as well as the parameterized complexity of other related problems. We give an O(nm+2dnm/ lgm) time algorithm for the uncolored variant of our biclique problem, where m is the number of areas of interest that are parsed from the target sequences, and n and d are as defined above. Our algorithm can be adapted to compute all maximal bicliques in the graph within the same time complexity, and to handle edge-weights with a slight O(lg d) increase to its time complexity. For the colored version of the problem, our algorithm has a time complexity of O(2dnm). We implement the algorithm and exemplify its application to LEE, a well-known pathogenicity island from the e. coli genome harboring virulence genes. Our code and supplementary materials, including omitted proofs and figures, are available at https://www. cs.bgu.ac.il/∼negevcb/RAGB/.

Original languageEnglish
Title of host publicationAlgorithms in Bioinformatics - 16th International Workshop, WABI 2016, Proceedings
EditorsMartin Frith, Christian Nørgaard Storm Pedersen
PublisherSpringer Verlag
Number of pages13
ISBN (Print)9783319436807
StatePublished - 1 Jan 2016
Event16th International Workshop on Algorithms in Bioinformatics, WABI 2016 - Aarhus, Denmark
Duration: 22 Aug 201624 Aug 2016

Publication series

NameLecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)
Volume9838 LNCS
ISSN (Print)0302-9743
ISSN (Electronic)1611-3349


Conference16th International Workshop on Algorithms in Bioinformatics, WABI 2016

ASJC Scopus subject areas

  • Theoretical Computer Science
  • General Computer Science


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