On the complexity of sparse exon assembly

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

Research output: Contribution to journalConference articlepeer-review

1 Scopus citations


Gene structure prediction is one of the most important problems in computational molecular biology. A combinatorial approach to the problem, denoted Gene Prediction via Spliced Alignment, was introduced by Gelfand, Mironov and Pevzner [5]. The method works by finding a set of blocks in a source genomic sequence S whose concatenation (splicing) fits a target gene T belonging to a homologous species. Let S,T and the candidate exons be sequences of size O(n). The innovative algorithm described in [5] yields an O(n 3) result for spliced alignment, regardless of filtration mode. In this paper we suggest a new algorithm which targets the 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 for this case.

Original languageEnglish
Pages (from-to)201-218
Number of pages18
JournalLecture Notes in Computer Science
StatePublished - 1 Jan 2005
Externally publishedYes
EventOt16th Annual Symposium on Combinatorial Pattern Matching, CPM 2005 - Jeju Island, Korea, Republic of
Duration: 19 Jun 200522 Jun 2005

ASJC Scopus subject areas

  • Theoretical Computer Science
  • General Computer Science


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