Efficient Alignment of RNAs with Pseudoknots Using Sequence Alignment Constraints
2009
Fast RNA Alignment with Pseudoknots
publication
10 minutes
Evidence: high
Author Information
Author(s): Yoon Byung-Jun
Primary Institution: Texas A&M University
Hypothesis
Can effective alignment constraints improve the speed and accuracy of RNA structural alignment algorithms?
Conclusion
The proposed method significantly speeds up RNA alignment without sacrificing accuracy.
Supporting Evidence
- The proposed method can speed up RNA alignment by up to 11 times.
- Using alignment constraints does not degrade the accuracy of RNA alignment.
- The method is particularly useful for aligning RNAs with complex structures like pseudoknots.
Takeaway
This study found a way to make comparing RNA sequences faster and just as accurate by using special rules for alignment.
Methodology
The study developed a new method using profile-HMMs to identify reliable seed regions for RNA alignment.
Limitations
The method may not perform well with very few training sequences.
Digital Object Identifier (DOI)
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