Lower bounds on multiple sequence alignment using exact 3-way alignment
2007
Improving Sequence Alignment with Lower Bounds
publication
Evidence: moderate
Author Information
Author(s): Colbourn Charles J, Kumar Sudhir
Primary Institution: Arizona State University
Hypothesis
Can lower bounds on multiple sequence alignment be improved using exact 3-way alignments?
Conclusion
Using a combination of 2-way and 3-way alignments can enhance the calculation of lower bounds on alignment costs.
Supporting Evidence
- Exact costs of optimum alignments are rarely computed due to exponential growth in computation time.
- Lower bounds can be calculated to assess the quality of the alignment.
- Employing a mixture of 3-way and 2-way alignments improves lower bounds on SP cost.
Takeaway
This study shows that by using some special methods, we can figure out how good our sequence alignments are without doing all the hard work.
Methodology
The study employs exact 2-way and 3-way alignments to compute lower bounds on total sum-of-pairs alignment cost.
Limitations
The methods may not be feasible for very large numbers of sequences due to computational complexity.
Digital Object Identifier (DOI)
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