Nucleic Acid Structure Prediction - Comparative Secondary Structure Prediction

Comparative Secondary Structure Prediction

Sequence covariation methods rely on the existence of a data set composed of multiple homologous RNA sequences with related but dissimilar sequences. These methods analyze the covariation of individual base sites in evolution; maintenance at two widely separated sites of a pair of base-pairing nucleotides indicates the presence of a structurally required hydrogen bond between those positions. The general problem of pseudoknot prediction has been shown to be NP-complete.

In general, the problem of alignment and consensus structure prediction are closely related. Three different approaches to the prediction of consensus structures can be distinguished:

  1. Folding of alignment
  2. Simultaneous sequence alignment and folding
  3. Alignment of predicted structures

Read more about this topic:  Nucleic Acid Structure Prediction

Famous quotes containing the words comparative, secondary, structure and/or prediction:

    “Our comparative fidelity was fear of defeat at the hands of another partner.”
    —Max Frisch (1911–1991)

    “Scientific reason, with its strict conscience, its lack of prejudice, and its determination to question every result again the moment it might lead to the least intellectual advantage, does in an area of secondary interest what we ought to be doing with the basic questions of life.”
    —Robert Musil (1880–1942)

    “Why does philosophy use concepts and why does faith use symbols if both try to express the same ultimate? The answer, of course, is that the relation to the ultimate is not the same in each case. The philosophical relation is in principle a detached description of the basic structure in which the ultimate manifests itself. The relation of faith is in principle an involved expression of concern about the meaning of the ultimate for the faithful.”
    —Paul Tillich (1886–1965)

    “Recent studies that have investigated maternal satisfaction have found this to be a better prediction of mother-child interaction than work status alone. More important for the overall quality of interaction with their children than simply whether the mother works or not, these studies suggest, is how satisfied the mother is with her role as worker or homemaker. Satisfied women are consistently more warm, involved, playful, stimulating and effective with their children than unsatisfied women.”
    —Alison Clarke-Stewart (20th century)