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Stratification of co-evolving genomic groups using ranked phylogenetic profiles.
Shiri Freilich1, Leon Goldovsky, Assaf Gottlieb
1The Blavatnik School of Computer Sciences and School of Medicine, Tel-Aviv University, Tel-Aviv 69978, Israel. shiri.freilich@gmail.com
BMC Bioinformatics
|October 29, 2009
Summary
Rank-BLAST accurately assigns protein sequences to their taxonomic origins using phylogenetic profiles. This novel method enhances genome analysis and metagenomics by improving species identification from sequence data.
Area of Science:
- Genomics
- Bioinformatics
- Computational Biology
Background:
- Traditional taxonomic origin detection relies on genome composition.
- Phylogenetic profiles offer an alternative but often lack accuracy.
- Novel methods are needed for robust taxonomic classification.
Purpose of the Study:
- Introduce rank-BLAST, a new approach for assigning protein sequences to taxonomic groups.
- Improve accuracy in determining the genomic origin of sequence collections.
- Enhance applications in genome analysis and metagenomics.
Main Methods:
- Utilizes the ranking order of phylogenetic profiles for target genes/proteins.
- Combines sequence searches, statistical estimation, and clustering.
- Analyzes sequence divergence to classify proteins by species of origin.
Main Results:
- Rank-BLAST achieves high accuracy in taxonomic classification, identifying the origin of 64% of studied proteins.
- Successfully classifies proteins from five distinct microbial species against a 243-genome database.
- Identifies main species clusters and distinct, functionally relevant secondary clusters.
Conclusions:
- Rank-BLAST provides an accurate and efficient method for determining taxonomic origins.
- The approach is valuable for genome evolution studies.
- Rank-BLAST significantly aids in identifying species groups within metagenomics samples.
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