Binding motif based code models for prokaryotic translation initiation

E. E. May; M. A. Vouk; D. L. Bitzer; D. I. Rosnick

doi:10.1109/ITAB.2003.1222399

Binding motif based code models for prokaryotic translation initiation

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

Research output: Chapter in Book/Report/Conference proceeding › Conference 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 language	English (US)
Title of host publication	Conference Proceedings - 4th International IEEE EMBS Special Topic Conference on Information Technology Applications in Biomedicine 2003
Subtitle of host publication	New Solutions for New Challenges, ITAB 2003
Publisher	Institute of Electrical and Electronics Engineers Inc.
Pages	5-8
Number of pages	4
ISBN (Electronic)	0780376676
DOIs	https://doi.org/10.1109/ITAB.2003.1222399
State	Published - 2003
Event	4th International IEEE EMBS Special Topic Conference on Information Technology Applications in Biomedicine 2003, ITAB 2003 - Birmingham, United Kingdom Duration: Apr 24 2003 → Apr 26 2003

Publication series

Name	Proceedings of the IEEE/EMBS Region 8 International Conference on Information Technology Applications in Biomedicine, ITAB
Volume	2003-January

Other

Other	4th International IEEE EMBS Special Topic Conference on Information Technology Applications in Biomedicine 2003, ITAB 2003
Country/Territory	United Kingdom
City	Birmingham
Period	4/24/03 → 4/26/03

Keywords

Coding Theory
Genetic Algorithms
Translation Initiation

ASJC Scopus subject areas

Computer Science Applications
Biomedical Engineering

Access to Document

10.1109/ITAB.2003.1222399

Cite this

May, E. E., Vouk, M. A., Bitzer, D. L., & Rosnick, D. I. (2003). Binding motif based code models for prokaryotic translation initiation. In Conference Proceedings - 4th International IEEE EMBS Special Topic Conference on Information Technology Applications in Biomedicine 2003: New Solutions for New Challenges, ITAB 2003 (pp. 5-8). Article 1222399 (Proceedings of the IEEE/EMBS Region 8 International Conference on Information Technology Applications in Biomedicine, ITAB; Vol. 2003-January). Institute of Electrical and Electronics Engineers Inc.. https://doi.org/10.1109/ITAB.2003.1222399

Binding motif based code models for prokaryotic translation initiation. / May, E. E.; Vouk, M. A.; Bitzer, D. L. et al.
Conference Proceedings - 4th International IEEE EMBS Special Topic Conference on Information Technology Applications in Biomedicine 2003: New Solutions for New Challenges, ITAB 2003. Institute of Electrical and Electronics Engineers Inc., 2003. p. 5-8 1222399 (Proceedings of the IEEE/EMBS Region 8 International Conference on Information Technology Applications in Biomedicine, ITAB; Vol. 2003-January).

Research output: Chapter in Book/Report/Conference proceeding › Conference contribution

May, EE, Vouk, MA, Bitzer, DL & Rosnick, DI 2003, Binding motif based code models for prokaryotic translation initiation. in Conference Proceedings - 4th International IEEE EMBS Special Topic Conference on Information Technology Applications in Biomedicine 2003: New Solutions for New Challenges, ITAB 2003., 1222399, Proceedings of the IEEE/EMBS Region 8 International Conference on Information Technology Applications in Biomedicine, ITAB, vol. 2003-January, Institute of Electrical and Electronics Engineers Inc., pp. 5-8, 4th International IEEE EMBS Special Topic Conference on Information Technology Applications in Biomedicine 2003, ITAB 2003, Birmingham, United Kingdom, 4/24/03. https://doi.org/10.1109/ITAB.2003.1222399

May EE, Vouk MA, Bitzer DL, Rosnick DI. Binding motif based code models for prokaryotic translation initiation. In Conference Proceedings - 4th International IEEE EMBS Special Topic Conference on Information Technology Applications in Biomedicine 2003: New Solutions for New Challenges, ITAB 2003. Institute of Electrical and Electronics Engineers Inc. 2003. p. 5-8. 1222399. (Proceedings of the IEEE/EMBS Region 8 International Conference on Information Technology Applications in Biomedicine, ITAB). doi: 10.1109/ITAB.2003.1222399

May, E. E. ; Vouk, M. A. ; Bitzer, D. L. et al. / Binding motif based code models for prokaryotic translation initiation. Conference Proceedings - 4th International IEEE EMBS Special Topic Conference on Information Technology Applications in Biomedicine 2003: New Solutions for New Challenges, ITAB 2003. Institute of Electrical and Electronics Engineers Inc., 2003. pp. 5-8 (Proceedings of the IEEE/EMBS Region 8 International Conference on Information Technology Applications in Biomedicine, ITAB).

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AB - 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.

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Binding motif based code models for prokaryotic translation initiation

Abstract

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Keywords

ASJC Scopus subject areas

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