Title :
Ensemble-based RNA secondary structure characterization (Engineering in Genomics)
Author :
Crozier, S.P. ; Garner, H.R.
Author_Institution :
Southwestern Med. Center, Texas Univ., Dallas, TX
Abstract :
We have presented here a method of characterizing the expected secondary structure or structures from a Boltzmann-weighted ensemble of such structures. In several applications of this method, the results provided structural insight not attainable by the use of free energy minimization methods. Previous approaches to characterizing the Boltzmann ensemble of structures have included the base-pairing probability profile as represented in the base pairing "dot plot" chart, the generation and examination of "suboptimal" structures and the visual examination of the Boltzmann ensemble of 1,000 structures. This method may be generally applicable to RNA secondary structure prediction and characterization and especially useful in automated applications
Keywords :
genetics; macromolecules; molecular biophysics; organic compounds; probability; Boltzmann-distribution; base-pairing probability profile; dot plot chart; ensemble-based RNA secondary structural characterization; free energy minimization method; genomics engineering; suboptimal structure; visual examination; Bioinformatics; Boltzmann distribution; Data engineering; Engineering in medicine and biology; Genomics; Minimization methods; Power engineering and energy; RNA; Sequences; Thermodynamics; Base Sequence; Computer Simulation; Models, Chemical; Models, Molecular; Molecular Sequence Data; Nucleic Acid Conformation; RNA; Sequence Alignment; Sequence Analysis, RNA;
Journal_Title :
Engineering in Medicine and Biology Magazine, IEEE
DOI :
10.1109/MEMB.2007.289125
