On the complexity of sparse exon assembly

Carmel Kent, Gad M. Landau, Michal Ziv-Ukelson

Research output: Contribution to journalArticlepeer-review


Gene structure prediction is one of the most important problems in computational molecular biology. It involves two steps: the first is finding the evidence (e.g., predicting splice sites) and the second is interpreting the evidence, that is, trying to determine the whole gene structure by assembling its pieces. In this paper, we suggest a combinatorial solution to the second step, which is also referred to as the "Exon Assembly Problem." We use a similarity-based approach that aims to produce a single gene structure based on similarities to a known homologous sequence. We target the sparse case, where filtering has been applied to the data, resulting in a set of O(n) candidate exon blocks. Our algorithm yields an O(n2 √n) solution.

Original languageEnglish
Pages (from-to)1013-1027
Number of pages15
JournalJournal of Computational Biology
Issue number5
StatePublished - Jun 2006


  • Dynamic programming
  • Exon assembly
  • Rectilinear Steiner arborescence
  • Sequence alignment

ASJC Scopus subject areas

  • Modeling and Simulation
  • Molecular Biology
  • Genetics
  • Computational Mathematics
  • Computational Theory and Mathematics


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