JaPaFi: A Tool for Finding Conserved DNA Sequences
Author Information
Author(s): Sadeque Aliya, Barsky Marina, Marass Francesco, Kruczkiewicz Peter, Upton Chris
Primary Institution: University of Victoria
Hypothesis
Is the conserved sequence element (CSE) unusually well conserved among different poxvirus genomes?
Conclusion
The study found that the CSE is part of a larger set of highly conserved sequences in poxvirus genomes, with many containing conserved promoter elements.
Supporting Evidence
- The JaPaFi tool can identify conserved sequences without needing to align genomes.
- The study identified 11 highly conserved sequences in seven poxvirus genomes.
- Most of the identified sequences are likely associated with viral promoters.
Takeaway
The researchers created a tool called JaPaFi to find important DNA sequences in viruses, and they discovered many similar sequences that help control how the virus works.
Methodology
The JaPaFi tool identifies short, highly conserved sequences in poxvirus genomes without requiring sequence alignment.
Limitations
The tool's scalability is limited to approximately 300,000 characters per input string.
Statistical Information
P-Value
1 × 10−3
Statistical Significance
p<0.001
Digital Object Identifier (DOI)
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