HiComet: a high-throughput comet analysis tool for large-scale DNA damage assessment
Abstract Background DNA damage causes aging, cancer, and other serious diseases. The comet assay can detect multiple types of DNA lesions with high sensitivity, and it has been widely applied. Although comet assay platforms have improved the limited throughput and reproducibility of traditional assa...
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| Format: | Article |
| Language: | English |
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BMC
2018-02-01
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| Series: | BMC Bioinformatics |
| Subjects: | |
| Online Access: | http://link.springer.com/article/10.1186/s12859-018-2015-7 |
| _version_ | 1811260024394088448 |
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| author | Taehoon Lee Sungmin Lee Woo Young Sim Yu Mi Jung Sunmi Han Joong-Ho Won Hyeyoung Min Sungroh Yoon |
| author_facet | Taehoon Lee Sungmin Lee Woo Young Sim Yu Mi Jung Sunmi Han Joong-Ho Won Hyeyoung Min Sungroh Yoon |
| author_sort | Taehoon Lee |
| collection | DOAJ |
| description | Abstract Background DNA damage causes aging, cancer, and other serious diseases. The comet assay can detect multiple types of DNA lesions with high sensitivity, and it has been widely applied. Although comet assay platforms have improved the limited throughput and reproducibility of traditional assays in recent times, analyzing large quantities of comet data often requires a tremendous human effort. To overcome this challenge, we proposed HiComet, a computational tool that can rapidly recognize and characterize a large number of comets, using little user intervention. Results We tested HiComet with real data from 35 high-throughput comet assay experiments, with over 700 comets in total. The proposed method provided unprecedented levels of performance as an automated comet recognition tool in terms of robustness (measured by precision and recall) and throughput. Conclusions HiComet is an automated tool for high-throughput comet-assay analysis and could significantly facilitate characterization of individual comets by accelerating its most rate-limiting step. An online implementation of HiComet is freely available at https://github.com/taehoonlee/HiComet/. |
| first_indexed | 2024-04-12T18:40:25Z |
| format | Article |
| id | doaj.art-29d7abdfc261485eafe1e5e8721848dd |
| institution | Directory Open Access Journal |
| issn | 1471-2105 |
| language | English |
| last_indexed | 2024-04-12T18:40:25Z |
| publishDate | 2018-02-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Bioinformatics |
| spelling | doaj.art-29d7abdfc261485eafe1e5e8721848dd2022-12-22T03:20:47ZengBMCBMC Bioinformatics1471-21052018-02-0119S1496110.1186/s12859-018-2015-7HiComet: a high-throughput comet analysis tool for large-scale DNA damage assessmentTaehoon Lee0Sungmin Lee1Woo Young Sim2Yu Mi Jung3Sunmi Han4Joong-Ho Won5Hyeyoung Min6Sungroh Yoon7Department of Electrical and Computer Engineering, Seoul National UniversityDepartment of Electrical and Computer Engineering, Seoul National UniversityR&D Center, Wearable HealthcareResearch Division, NanoEnTekResearch Division, NanoEnTekDepartment of Statistics, Seoul National UniversityCollege of Pharmachy, Chung-Ang UniversityDepartment of Electrical and Computer Engineering, Seoul National UniversityAbstract Background DNA damage causes aging, cancer, and other serious diseases. The comet assay can detect multiple types of DNA lesions with high sensitivity, and it has been widely applied. Although comet assay platforms have improved the limited throughput and reproducibility of traditional assays in recent times, analyzing large quantities of comet data often requires a tremendous human effort. To overcome this challenge, we proposed HiComet, a computational tool that can rapidly recognize and characterize a large number of comets, using little user intervention. Results We tested HiComet with real data from 35 high-throughput comet assay experiments, with over 700 comets in total. The proposed method provided unprecedented levels of performance as an automated comet recognition tool in terms of robustness (measured by precision and recall) and throughput. Conclusions HiComet is an automated tool for high-throughput comet-assay analysis and could significantly facilitate characterization of individual comets by accelerating its most rate-limiting step. An online implementation of HiComet is freely available at https://github.com/taehoonlee/HiComet/.http://link.springer.com/article/10.1186/s12859-018-2015-7Comet assaySingle cell electrophoresisImage processingSegmentation |
| spellingShingle | Taehoon Lee Sungmin Lee Woo Young Sim Yu Mi Jung Sunmi Han Joong-Ho Won Hyeyoung Min Sungroh Yoon HiComet: a high-throughput comet analysis tool for large-scale DNA damage assessment BMC Bioinformatics Comet assay Single cell electrophoresis Image processing Segmentation |
| title | HiComet: a high-throughput comet analysis tool for large-scale DNA damage assessment |
| title_full | HiComet: a high-throughput comet analysis tool for large-scale DNA damage assessment |
| title_fullStr | HiComet: a high-throughput comet analysis tool for large-scale DNA damage assessment |
| title_full_unstemmed | HiComet: a high-throughput comet analysis tool for large-scale DNA damage assessment |
| title_short | HiComet: a high-throughput comet analysis tool for large-scale DNA damage assessment |
| title_sort | hicomet a high throughput comet analysis tool for large scale dna damage assessment |
| topic | Comet assay Single cell electrophoresis Image processing Segmentation |
| url | http://link.springer.com/article/10.1186/s12859-018-2015-7 |
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