Cov-trans: an efficient algorithm for discontinuous transcript assembly in coronaviruses.

Cov-trans: an efficient algorithm for discontinuous transcript assembly in coronaviruses.

Publication date: Dec 30, 2024

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. 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. 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 .

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Concepts Keywords
Antiviral Coronaviruses
Bioinfo Discontinuous transcription
Coronaviruses Referenced-based assembly
Efficient
Integer

Semantics

Type Source Name
disease IDO algorithm
disease IDO host
drug DRUGBANK Coenzyme M
pathway REACTOME Reproduction
drug DRUGBANK Trestolone
pathway REACTOME Methylation
pathway REACTOME Translation
disease IDO process
disease MESH infection
disease IDO quality
drug DRUGBANK Esomeprazole
disease IDO protein
drug DRUGBANK Cytidine-5′-Monophosphate
drug DRUGBANK Aspartame
drug DRUGBANK Ademetionine
drug DRUGBANK Pentaerythritol tetranitrate
disease IDO cell
drug DRUGBANK Chlorcyclizine

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