Binding motif based code models for prokaryotic translation initiation

Elebeoba May, M. A. Vouk, D. L. Bitzer, D. I. Rosnick

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

Abstract

Studies of prokaryotic translation initiation sites reveal that ribosomal binding sites appear to evolve to functional requirements rather than to genetic sequences that produce the strongest binding site. Several factors influence translation of mRNA sequences, including: initiation codon, presence and location of the Shine-Dalgarno sequence, spacing between the initiation codon and the Shine-Dalgarno domain, the second codon following the initiator codon, and possibly other nucleotides in the-20 to +13 region of the mRNA leader region. These factors influence how the small subunit of the ribosome interacts with and binds to the mRNA leader region such that conditions are favorable for successful translation initiation. In this work translation initiation models are constructed by analyzing possible binding patterns between mRNA leader sequences and the exposed portion of the 16S rRNA. Binding analysis data are used as inputs to a genetic algorithm which searches for optimal binary, convolutional codes to model the Eschericha coli K-12 translation initiation system. We present an evaluation of the coding models discovered.

Original languageEnglish (US)
Title of host publicationProceedings of the IEEE/EMBS Region 8 International Conference on Information Technology Applications in Biomedicine, ITAB
PublisherInstitute of Electrical and Electronics Engineers Inc.
Pages5-8
Number of pages4
Volume2003-January
ISBN (Print)0780376676
DOIs
StatePublished - 2003
Event4th International IEEE EMBS Special Topic Conference on Information Technology Applications in Biomedicine 2003, ITAB 2003 - Birmingham, United Kingdom
Duration: Apr 24 2003Apr 26 2003

Other

Other4th International IEEE EMBS Special Topic Conference on Information Technology Applications in Biomedicine 2003, ITAB 2003
CountryUnited Kingdom
CityBirmingham
Period4/24/034/26/03

Keywords

  • Coding Theory
  • Genetic Algorithms
  • Translation Initiation

ASJC Scopus subject areas

  • Computer Science Applications
  • Biomedical Engineering

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