A stitch in time: Efficient computation of genomic DNA melting bubbles

@article{Tstesen2008ASI,
  title={A stitch in time: Efficient computation of genomic DNA melting bubbles},
  author={Eivind T{\o}stesen},
  journal={Algorithms for Molecular Biology : AMB},
  year={2008},
  volume={3},
  pages={10 - 10}
}
  • E. Tøstesen
  • Published 7 February 2008
  • Computer Science
  • Algorithms for Molecular Biology : AMB
BackgroundIt is of biological interest to make genome-wide predictions of the locations of DNA melting bubbles using statistical mechanics models. Computationally, this poses the challenge that a generic search through all combinations of bubble starts and ends is quadratic.ResultsAn efficient algorithm is described, which shows that the time complexity of the task is O(NlogN) rather than quadratic. The algorithm exploits that bubble lengths may be limited, but without a prior assumption of a… 

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References

SHOWING 1-10 OF 85 REFERENCES

Speed-up of DNA melting algorithm with complete nearest neighbor properties.

An optimized algorithm is described, which is faster and more accurate compared to previously described algorithms, for computing the statistical mechanics of denaturation of nucleic acid sequences according to the classical Poland-Scheraga type of model and is proposed to use to calculate various other probabilities for a more direct view of the melting regions and their positions and sizes.

Reparametrizing the loop entropy weights: effect on DNA melting curves.

  • R. BlosseyE. Carlon
  • Biology
    Physical review. E, Statistical, nonlinear, and soft matter physics
  • 2003
It is argued that in the melting region the double helix persistence length is greatly reduced compared to its room temperature value, so that the use of the embedded loop closure exponent for real DNA sequences is justified.

Breathing dynamics in heteropolymer DNA.

The strong dependence on sequence, temperature and salt concentration for the breathing dynamics of DNA found here points at a good potential for nanosensing applications by utilizing short fluorophore-quencher dressed DNA constructs.

The Human Genomic Melting Map

A melting map calculation is applied to the complete human genome, which provides information about the propensities of forming local bubbles determined from the whole sequence, and a first report on its basic features, the extent of cooperativity, and correlations to various physical and biological features of the human genome is presented.

DNA dynamically directs its own transcription initiation.

This work shows that the Peyrard-Bishop nonlinear dynamical model of DNA gives an accurate representation of the instability profile of a defined sequence of DNA, as verified using S1 nuclease cleavage assays.

The physics of DNA and the annotation of the Plasmodium falciparum genome.

Stitchprofiles.uio.no: analysis of partly melted DNA conformations using stitch profiles

A web server that performs computations on DNA melting, thus predicting the localized separation of the two strands for sequences provided by the users, and the output types are stitch profiles, melting curves, probability profiles, etc.

Theory of DNA melting curves

It is shown that a decomposition of the loop entropy factor into a sum of I exponential functions gives an extremely accurate approximation to theloop entropy factor for small values of I and makes the computer time for the exact algorithms proportional to I·N proportional to N.

Partly melted DNA conformations obtained with a probability peak finding method.

  • E. Tøstesen
  • Mathematics
    Physical review. E, Statistical, nonlinear, and soft matter physics
  • 2005
Peaks in the probabilities of loops or bubbles, helical segments, and unzipping ends in melting DNA are found in this article using a peak finding method that maps the hierarchical structure of

Genes and the physics of the DNA double-helix.

...