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Face of Tobias Ambjörnsson. Photo.

Tobias Ambjörnsson

Senior lecturer

Face of Tobias Ambjörnsson. Photo.

Noise reduction in single time frame optical DNA maps

Author

  • Paola C. Torche Pedreschi
  • Vilhelm Müller
  • Fredrik Westerlund
  • Tobias Ambjörnsson

Summary, in English

In optical DNA mapping technologies sequence-specific intensity variations (DNA barcodes) along stretched and stained DNA molecules are produced. These "fingerprints" of the underlying DNA sequence have a resolution of the order one kilobasepairs and the stretching of the DNA molecules are performed by surface adsorption or nano-channel setups. A postprocessing challenge for nano-channel based methods, due to local and global random movement of the DNA molecule during imaging, is how to align different time frames in order to produce reproducible time-averaged DNA barcodes. The current solutions to this challenge are computationally rather slow. With high-throughput applications in mind, we here introduce a parameter-free method for filtering a single time frame noisy barcode (snap-shot optical map), measured in a fraction of a second. By using only a single time frame barcode we circumvent the need for post-processing alignment. We demonstrate that our method is successful at providing filtered barcodes which are less noisy and more similar to time averaged barcodes. The method is based on the application of a low-pass filter on a single noisy barcode using the width of the Point Spread Function of the system as a unique, and known, filtering parameter. We find that after applying our method, the Pearson correlation coefficient (a real number in the range from -1 to 1) between the single time-frame barcode and the time average of the aligned kymograph increases significantly, roughly by 0.2 on average. By comparing to a database of more than 3000 theoretical plasmid barcodes we show that the capabilities to identify plasmids is improved by filtering single time-frame barcodes compared to the unfiltered analogues. Since snap-shot experiments and computational time using our method both are less than a second, this study opens up for high throughput optical DNA mapping with improved reproducibility.

Department/s

  • Department of Astronomy and Theoretical Physics

Publishing year

2017-06-01

Language

English

Publication/Series

PLoS ONE

Volume

12

Issue

6

Document type

Journal article

Publisher

Public Library of Science

Topic

  • Biophysics

Status

Published

ISBN/ISSN/Other

  • ISSN: 1932-6203