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Statistical analysis of RNA backbone.

Publication ,  Journal Article
Hershkovitz, E; Sapiro, G; Tannenbaum, A; Williams, LD
Published in: IEEE/ACM transactions on computational biology and bioinformatics
January 2006

Local conformation is an important determinant of RNA catalysis and binding. The analysis of RNA conformation is particularly difficult due to the large number of degrees of freedom (torsion angles) per residue. Proteins, by comparison, have many fewer degrees of freedom per residue. In this work, we use and extend classical tools from statistics and signal processing to search for clusters in RNA conformational space. Results are reported both for scalar analysis, where each torsion angle is separately studied, and for vectorial analysis, where several angles are simultaneously clustered. Adapting techniques from vector quantization and clustering to the RNA structure, we find torsion angle clusters and RNA conformational motifs. We validate the technique using well-known conformational motifs, showing that the simultaneous study of the total torsion angle space leads to results consistent with known motifs reported in the literature and also to the finding of new ones.

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Published In

IEEE/ACM transactions on computational biology and bioinformatics

DOI

EISSN

1557-9964

ISSN

1545-5963

Publication Date

January 2006

Volume

3

Issue

1

Start / End Page

33 / 46

Related Subject Headings

  • Sequence Analysis, RNA
  • RNA
  • Nucleic Acid Conformation
  • Molecular Sequence Data
  • Models, Statistical
  • Models, Molecular
  • Models, Chemical
  • Data Interpretation, Statistical
  • Computer Simulation
  • Bioinformatics
 

Citation

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Hershkovitz, E., Sapiro, G., Tannenbaum, A., & Williams, L. D. (2006). Statistical analysis of RNA backbone. IEEE/ACM Transactions on Computational Biology and Bioinformatics, 3(1), 33–46. https://doi.org/10.1109/tcbb.2006.13
Hershkovitz, Eli, Guillermo Sapiro, Allen Tannenbaum, and Loren Dean Williams. “Statistical analysis of RNA backbone.IEEE/ACM Transactions on Computational Biology and Bioinformatics 3, no. 1 (January 2006): 33–46. https://doi.org/10.1109/tcbb.2006.13.
Hershkovitz E, Sapiro G, Tannenbaum A, Williams LD. Statistical analysis of RNA backbone. IEEE/ACM transactions on computational biology and bioinformatics. 2006 Jan;3(1):33–46.
Hershkovitz, Eli, et al. “Statistical analysis of RNA backbone.IEEE/ACM Transactions on Computational Biology and Bioinformatics, vol. 3, no. 1, Jan. 2006, pp. 33–46. Epmc, doi:10.1109/tcbb.2006.13.
Hershkovitz E, Sapiro G, Tannenbaum A, Williams LD. Statistical analysis of RNA backbone. IEEE/ACM transactions on computational biology and bioinformatics. 2006 Jan;3(1):33–46.

Published In

IEEE/ACM transactions on computational biology and bioinformatics

DOI

EISSN

1557-9964

ISSN

1545-5963

Publication Date

January 2006

Volume

3

Issue

1

Start / End Page

33 / 46

Related Subject Headings

  • Sequence Analysis, RNA
  • RNA
  • Nucleic Acid Conformation
  • Molecular Sequence Data
  • Models, Statistical
  • Models, Molecular
  • Models, Chemical
  • Data Interpretation, Statistical
  • Computer Simulation
  • Bioinformatics