title: Automated DNA fragments recognition and sizing through AFM image processing.
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%.
authors.affiliation: Politecnico di Torino, DAUIN, Italy. elisa.ficarra@polito.it
authors.forename: Elisa
authors.initials: E
authors.lastname: Ficarra
authors.forename: Luca
authors.initials: L
authors.lastname: Benini
authors.forename: Enrico
authors.initials: E
authors.lastname: Macii
authors.forename: Giampaolo
authors.initials: G
authors.lastname: Zuccheri
mesh_terms: D000465:Algorithms; D001185:Artificial Intelligence; D004247:DNA / Q000032:analysis / Q000737:chemistry* / Q000648:ultrastructure*; D016172:DNA Fingerprinting / Q000379:methods*; D053938:DNA Fragmentation; D007089:Image Enhancement / Q000379:methods; D007090:Image Interpretation, Computer-Assisted / Q000379:methods*; D021621:Imaging, Three-Dimensional / Q000379:methods*; D018625:Microscopy, Atomic Force / Q000379:methods*; D015394:Molecular Structure; D009690:Nucleic Acid Conformation; D010316:Particle Size; D010363:Pattern Recognition, Automated / Q000379:methods*
chemical_list: D004247:DNA