New Algorithm for Protein Conservation Profiles
Author Information
Author(s): John K. Vries, Xiong Liu
Primary Institution: Department of Computational Biology, School of Medicine, University of Pittsburgh
Hypothesis
Can a new algorithm based on n-gram patterns generate accurate conservation profiles for protein subfamilies?
Conclusion
The new algorithm can generate subfamily specific conservation profiles without prior knowledge of family relationships or domain architecture.
Supporting Evidence
- The algorithm was able to construct 4,248 profiles from 120 randomly selected Pfam-A families.
- The speed of the new algorithm was comparable to the multiple alignment approach.
- Subfamily specific conservation profiles can be generated even for subfamilies with as few as five members.
Takeaway
Scientists created a new way to look at protein families that helps them understand how similar they are, even if they don't have a lot of examples to compare.
Methodology
The algorithm uses n-gram patterns and singular value decomposition to differentiate signal from noise in protein sequences.
Limitations
The algorithm may not perform well for very small protein families with fewer than five members.
Digital Object Identifier (DOI)
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