Resonance restriction technique for the resolution-based retrieval of palindrome in escherichia coli genome sequence

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Abstract

In this paper we propose a novel biological reasoning technique to find genetic palindrome using the resolution- based ATP (automated theorem proving) computing strategy. To retrieve the palindromic sequence, we apply automated deduction software with some resolution strategies to increase program performance. While the conventional reasoning or logic programming oriented method is basically top-down process, our method is bottom-up, resolution-based and also enhanced by direction and restriction reasoning strategies. Proposal method is divided into two steps. First, each element of sequence is represented as one state clause. Second, biological reasoning program resolve these states to retrieve palindrome motif from genetic sequence. Besides, to make this resolution process faster, we apply a reasoning strategy called resonance restriction. This resolution strategy blocks the biological reasoning by avoiding expression that do not mach the patterns set by researchers. This pattern is called “resonator” which is expressed by symbol patterns in automated reasoning. In our model, researcher assigns resonators to the gap between repeated regions which prevent his program from redundant search related non-symmetric parts of genetic sequence. Resonators restrict discovery process by discarding clauses generated around the gap between palindromic motifs, which enhance sharply the performance of reasoning program. In experiment, we translate whole genome sequence of Escherichia coli into clausal representation. Numerical results are presented about the retrieval of palindrome in Escherichia coli to valid the effectiveness of proposal technique. We validate that resonance restriction makes reasoning process faster with experimental output of generated clauses, CPU time.

Original languageEnglish
Title of host publicationIFMBE Proceedings
PublisherSpringer Verlag
Pages205-208
Number of pages4
Volume14
Edition1
Publication statusPublished - 2007
Event10th World Congress on Medical Physics and Biomedical Engineering, WC 2006 - Seoul, Korea, Republic of
Duration: 2006 Aug 272006 Sep 1

Other

Other10th World Congress on Medical Physics and Biomedical Engineering, WC 2006
CountryKorea, Republic of
CitySeoul
Period06/8/2706/9/1

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Keywords

  • Biological reasoning
  • Escherichia coli genome sequence
  • Finding palindrome
  • Resolution-based retrieval
  • Resonance-restriction strategy

ASJC Scopus subject areas

  • Biomedical Engineering
  • Bioengineering

Cite this

Ando, R., & Takefuji, Y. (2007). Resonance restriction technique for the resolution-based retrieval of palindrome in escherichia coli genome sequence. In IFMBE Proceedings (1 ed., Vol. 14, pp. 205-208). Springer Verlag.