1. Academic Validation
  2. Automatic DNA replication tract measurement to assess replication and repair dynamics at the single molecule level

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

  • Bioinformatics. 2022 Jul 26;38(18):4395-4402. doi: 10.1093/bioinformatics/btac533.
Longjie Li 1 2 Arun Mouli Kolinjivadi 3 Kok Haur Ong 1 2 David Young 1 4 Gabriel Pik Liang Marini 2 Sock Hoai Chan 5 6 Siao Ting Chong 3 Ee Ling Chew 5 Haoda Lu 2 Laurent Gole 1 Weimiao Yu 1 2 Joanne Ngeow 3 5 6
Affiliations

Affiliations

  • 1 Institute of Molecular and Cell Biology, A*STAR, Singapore, 138673.
  • 2 Bioinformatics Institute, A*STAR, Singapore, 138671.
  • 3 Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, 308232.
  • 4 Department of Psychiatry and Behavioral Sciences, UCSF Weill Institute for Neurosciences, University of California, San Francisco, United States.
  • 5 Cancer Genetics Service, Division of Medical Oncology, National Cancer Centre, Singapore, 169610.
  • 6 Oncology Academic Clinical Program, Duke-NUS Medical School Singapore, Singapore, 169857.
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 recognise 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 6 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: The software package is available at https://github.com/lgole/DNAStranding.

Supplementary information: Supplementary data are available at Bioinformatics online.

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  • Cat. No.
    Product Name
    Description
    Target
    Research Area
  • HY-16106
    99.89%, PARP Inhibitor