This paper presents an automated algorithm to determine DNA fragment size from atomic force microscope images and to extract the molecular profiles. The sizing of DNA fragments is a widely used procedure for investigating the physical properties of individual or protein-bound DNA molecules. Several atomic force microscope (AFM) real and computer-generated images were tested for different pixel and fragment sizes and for different background noises. The automated approach minimizes processing time with respect to manual and semi-automated DNA sizing. Moreover, the DNA molecule profile recognition can be used to perform further structural analysis. For computer-generated images, the root mean square error incurred by the automated algorithm in the length estimation is 0.6% for a 7.8 nm image pixel size and 0.34% for a 3.9 nm image pixel size. For AFM real images we obtain a distribution of lengths with a standard deviation of 2.3% of mean and a measured average length very close to the real one, with an error around 0.33%.

Automated DNA Fragments Recognition and Sizing through AFM Image Processing / Ficarra, Elisa; Benini, L; Macii, Enrico; Zuccheri, G.. - In: IEEE TRANSACTIONS ON INFORMATION TECHNOLOGY IN BIOMEDICINE. - ISSN 1089-7771. - 9:4(2005), pp. 508-517. [10.1109/TITB.2005.855546]

Automated DNA Fragments Recognition and Sizing through AFM Image Processing

FICARRA, ELISA;
2005

Abstract

This paper presents an automated algorithm to determine DNA fragment size from atomic force microscope images and to extract the molecular profiles. The sizing of DNA fragments is a widely used procedure for investigating the physical properties of individual or protein-bound DNA molecules. Several atomic force microscope (AFM) real and computer-generated images were tested for different pixel and fragment sizes and for different background noises. The automated approach minimizes processing time with respect to manual and semi-automated DNA sizing. Moreover, the DNA molecule profile recognition can be used to perform further structural analysis. For computer-generated images, the root mean square error incurred by the automated algorithm in the length estimation is 0.6% for a 7.8 nm image pixel size and 0.34% for a 3.9 nm image pixel size. For AFM real images we obtain a distribution of lengths with a standard deviation of 2.3% of mean and a measured average length very close to the real one, with an error around 0.33%.
2005
9
4
508
517
Automated DNA Fragments Recognition and Sizing through AFM Image Processing / Ficarra, Elisa; Benini, L; Macii, Enrico; Zuccheri, G.. - In: IEEE TRANSACTIONS ON INFORMATION TECHNOLOGY IN BIOMEDICINE. - ISSN 1089-7771. - 9:4(2005), pp. 508-517. [10.1109/TITB.2005.855546]
Ficarra, Elisa; Benini, L; Macii, Enrico; Zuccheri, G.
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Utilizza questo identificativo per citare o creare un link a questo documento: https://hdl.handle.net/11380/1240372
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