Noise reduction in single time frame optical DNA maps
(2017) In PLoS ONE 12(6).- Abstract
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... (More)
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.
(Less)
- author
- Torche Pedreschi, Paola C. ; Müller, Vilhelm ; Westerlund, Fredrik and Ambjörnsson, Tobias LU
- organization
- publishing date
- 2017-06-01
- type
- Contribution to journal
- publication status
- published
- subject
- in
- PLoS ONE
- volume
- 12
- issue
- 6
- article number
- e0179041
- publisher
- Public Library of Science (PLoS)
- external identifiers
-
- pmid:28640821
- wos:000404135800016
- scopus:85021220863
- ISSN
- 1932-6203
- DOI
- 10.1371/journal.pone.0179041
- language
- English
- LU publication?
- yes
- id
- d910784c-4e86-484f-b2aa-f840e7c1d163
- date added to LUP
- 2017-08-30 10:38:34
- date last changed
- 2024-03-17 19:45:18
@article{d910784c-4e86-484f-b2aa-f840e7c1d163,
abstract = {{<p>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.</p>}},
author = {{Torche Pedreschi, Paola C. and Müller, Vilhelm and Westerlund, Fredrik and Ambjörnsson, Tobias}},
issn = {{1932-6203}},
language = {{eng}},
month = {{06}},
number = {{6}},
publisher = {{Public Library of Science (PLoS)}},
series = {{PLoS ONE}},
title = {{Noise reduction in single time frame optical DNA maps}},
url = {{http://dx.doi.org/10.1371/journal.pone.0179041}},
doi = {{10.1371/journal.pone.0179041}},
volume = {{12}},
year = {{2017}},
}