PHOG-BLAST – a new generation tool for fast similarity search of protein families
2006
PHOG-BLAST: A Fast Tool for Protein Family Similarity Search
publication
Evidence: moderate
Author Information
Author(s): Igor V Merkeev, Andrey A Mironov
Primary Institution: State Scientific Center GosNIIGenetica, Moscow State University
Hypothesis
Can a new algorithm improve the speed and efficiency of comparing protein families?
Conclusion
PHOG-BLAST is significantly faster and requires less memory than existing algorithms while maintaining comparable performance.
Supporting Evidence
- PHOG-BLAST required 10–20 times less computer memory and computation time than PSI-BLAST.
- On the COG database, both PHOG-BLAST and PSI-BLAST showed the same performance.
- PHOG-BLAST helped build the PHOG database of phylogenetic orthologous groups.
Takeaway
PHOG-BLAST is a new tool that helps scientists quickly compare proteins, making it easier to study how they are related.
Methodology
The algorithm uses profile discretization and hashing for fast similarity searches of protein profiles.
Limitations
PHOG-BLAST is less precise than rigorous methods for detecting weak similarities between protein families.
Digital Object Identifier (DOI)
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