Automatic DNA replication tract measurement to assess replication and repair dynamics at the single-molecule level

• Published in: Bioinformatics Vol. 38; no. 18; pp. 4395 - 4402
• Main Authors: Li, Longjie, Kolinjivadi, Arun Mouli, Ong, Kok Haur, Young, David M, Marini, Gabriel Pik Liang, Chan, Sock Hoai, Chong, Siao Ting, Chew, Ee Ling, Lu, Haoda, Gole, Laurent, Yu, Weimiao, Ngeow, Joanne
• Format: Journal Article
• Language: English
• Published: England Oxford University Press 15-09-2022
• Subjects: DNA; DNA Replication; Original Papers; Software; Workflow
• ISSN: 1367-4803; 1460-2059; 1367-4811
• DOI: 10.1093/bioinformatics/btac533

Abstract
Motivation
DNA fibre assay has a potential application in genomic medicine, cancer and stem cell research at the single-molecule level. A major challenge for the clinical and research implementation of DNA fibre assays is the slow speed in which manual analysis takes place as it limits the clinical actionability. While automatic detection of DNA fibres speeds up this process considerably, current publicly available software have limited features in terms of their user interface for manual correction of results, which in turn limit their accuracy and ability to account for atypical structures that may be important in diagnosis or investigative studies. We recognize that core improvements can be made to the GUI to allow for direct interaction with automatic results to preserve accuracy as well as enhance the versatility of automatic DNA fibre detection for use in variety of situations.
Results
To address the unmet needs of diverse DNA fibre analysis investigations, we propose DNA Stranding, an open-source software that is able to perform accurate fibre length quantification (13.22% mean relative error) and fibre pattern recognition (R > 0.93) with up to six fibre patterns supported. With the graphical interface, we developed, user can conduct semi-automatic analyses which benefits from the advantages of both automatic and manual processes to improve workflow efficiency without compromising accuracy.
Availability and implementation
The software package is available at https://github.com/lgole/DNAStranding.
Supplementary information
Supplementary data are available at Bioinformatics online.