A Biclique Approach to Reference Anchored Gene Blocks and Its Applications to Pathogenicity Islands

  title={A Biclique Approach to Reference Anchored Gene Blocks and Its Applications to Pathogenicity Islands},
  author={Arnon Benshahar and Vered Chalifa-Caspi and Danny Hermelin and Michal Ziv-Ukelson},
  booktitle={Workshop on Algorithms in Bioinformatics},
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 \(\mathcal {T}=\{T_1 \ldots T_c\}\). Our objective is to identify gene-blocks in \(\mathcal {T}\) that are centered in a subset q of co-localized genes from Q, and contain genomes from \(\mathcal {T}\) in… 



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