Cov-trans: an efficient algorithm for discontinuous transcript assembly in coronaviruses
Abstract Background Discontinuous transcription allows coronaviruses to efficiently replicate and transmit within host cells, enhancing their adaptability and survival. Assembling viral transcripts is crucial for virology research and the development of antiviral strategies. However, traditional tra...
Saved in:
| Main Authors: | , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
BMC
2024-12-01
|
| Series: | BMC Genomics |
| Subjects: | |
| Online Access: | https://doi.org/10.1186/s12864-024-11179-0 |
| Tags: |
Add Tag
No Tags, Be the first to tag this record!
|
| _version_ | 1841559811170238464 |
|---|---|
| author | Xiaoyu Guo Zhenming Wu Shu Zhang Jin Zhao |
| author_facet | Xiaoyu Guo Zhenming Wu Shu Zhang Jin Zhao |
| author_sort | Xiaoyu Guo |
| collection | DOAJ |
| description | Abstract Background Discontinuous transcription allows coronaviruses to efficiently replicate and transmit within host cells, enhancing their adaptability and survival. Assembling viral transcripts is crucial for virology research and the development of antiviral strategies. However, traditional transcript assembly methods primarily designed for variable alternative splicing events in eukaryotes are not suitable for the viral transcript assembly problem. The current algorithms designed for assembling viral transcripts often struggle with low accuracy in determining the transcript boundaries. There is an urgent need to develop a highly accurate viral transcript assembly algorithm. Results In this work, we propose Cov-trans, a reference-based transcript assembler specifically tailored for the discontinuous transcription of coronaviruses. Cov-trans first identifies canonical transcripts based on discontinuous transcription mechanisms, start and stop codons, as well as reads alignment information. Subsequently, it formulates the assembly of non-canonical transcripts as a path extraction problem, and introduces a mixed integer linear programming to recover these non-canonical transcripts. Conclusion Experimental results show that Cov-trans outperforms other assemblers in both accuracy and recall, with a notable strength in accurately identifying the boundaries of transcripts. Cov-trans is freely available at https://github.com/computer-Bioinfo/Cov-trans.git . |
| format | Article |
| id | doaj-art-63d288044be54ceebcfc0be0e8424028 |
| institution | Kabale University |
| issn | 1471-2164 |
| language | English |
| publishDate | 2024-12-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Genomics |
| spelling | doaj-art-63d288044be54ceebcfc0be0e84240282025-01-05T12:09:26ZengBMCBMC Genomics1471-21642024-12-0125111110.1186/s12864-024-11179-0Cov-trans: an efficient algorithm for discontinuous transcript assembly in coronavirusesXiaoyu Guo0Zhenming Wu1Shu Zhang2Jin Zhao3School of Computer Science and Technology, Qingdao UniversitySchool of Computer Science and Technology, Qingdao UniversitySchool of Computer Science and Technology, Qingdao UniversitySchool of Computer Science and Technology, Qingdao UniversityAbstract Background Discontinuous transcription allows coronaviruses to efficiently replicate and transmit within host cells, enhancing their adaptability and survival. Assembling viral transcripts is crucial for virology research and the development of antiviral strategies. However, traditional transcript assembly methods primarily designed for variable alternative splicing events in eukaryotes are not suitable for the viral transcript assembly problem. The current algorithms designed for assembling viral transcripts often struggle with low accuracy in determining the transcript boundaries. There is an urgent need to develop a highly accurate viral transcript assembly algorithm. Results In this work, we propose Cov-trans, a reference-based transcript assembler specifically tailored for the discontinuous transcription of coronaviruses. Cov-trans first identifies canonical transcripts based on discontinuous transcription mechanisms, start and stop codons, as well as reads alignment information. Subsequently, it formulates the assembly of non-canonical transcripts as a path extraction problem, and introduces a mixed integer linear programming to recover these non-canonical transcripts. Conclusion Experimental results show that Cov-trans outperforms other assemblers in both accuracy and recall, with a notable strength in accurately identifying the boundaries of transcripts. Cov-trans is freely available at https://github.com/computer-Bioinfo/Cov-trans.git .https://doi.org/10.1186/s12864-024-11179-0Referenced-based assemblyMixed integer linear programmingDiscontinuous transcriptionCoronaviruses |
| spellingShingle | Xiaoyu Guo Zhenming Wu Shu Zhang Jin Zhao Cov-trans: an efficient algorithm for discontinuous transcript assembly in coronaviruses BMC Genomics Referenced-based assembly Mixed integer linear programming Discontinuous transcription Coronaviruses |
| title | Cov-trans: an efficient algorithm for discontinuous transcript assembly in coronaviruses |
| title_full | Cov-trans: an efficient algorithm for discontinuous transcript assembly in coronaviruses |
| title_fullStr | Cov-trans: an efficient algorithm for discontinuous transcript assembly in coronaviruses |
| title_full_unstemmed | Cov-trans: an efficient algorithm for discontinuous transcript assembly in coronaviruses |
| title_short | Cov-trans: an efficient algorithm for discontinuous transcript assembly in coronaviruses |
| title_sort | cov trans an efficient algorithm for discontinuous transcript assembly in coronaviruses |
| topic | Referenced-based assembly Mixed integer linear programming Discontinuous transcription Coronaviruses |
| url | https://doi.org/10.1186/s12864-024-11179-0 |
| work_keys_str_mv | AT xiaoyuguo covtransanefficientalgorithmfordiscontinuoustranscriptassemblyincoronaviruses AT zhenmingwu covtransanefficientalgorithmfordiscontinuoustranscriptassemblyincoronaviruses AT shuzhang covtransanefficientalgorithmfordiscontinuoustranscriptassemblyincoronaviruses AT jinzhao covtransanefficientalgorithmfordiscontinuoustranscriptassemblyincoronaviruses |