On K-peptide length in composition vector phylogeny of prokaryotes

Using an enlarged alphabet of K-tuples is the way to carry out alignment-free comparison of genomes in the composition vector (CV) approach to prokaryotic phylogeny. We summarize the known aspects concerning the choice of K and examine the results of using CVs with subtraction of a statistical backg...

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Bibliographic Details
Published in:Computational biology and chemistry 2014-12, Vol.53, p.166-173
Main Authors: Zuo, Guanghong, Li, Qiang, Hao, Bailin
Format: Article
Language:English
Subjects:
Algorithms
Alignment-free
Archaea - classification
Archaea - genetics
Archaeal Proteins - chemistry
Archaeal Proteins - genetics
Bacteria - classification
Bacteria - genetics
Bacterial Proteins - chemistry
Bacterial Proteins - genetics
Composition vector
Genome, Archaeal
Genome, Bacterial
Peptides - chemistry
Peptides - genetics
Phylogeny
Prokaryote phylogeny and taxonomy
Sequence Analysis, DNA
Sequence Analysis, Protein
Subtraction procedure
Whole-genome-based
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Summary:Using an enlarged alphabet of K-tuples is the way to carry out alignment-free comparison of genomes in the composition vector (CV) approach to prokaryotic phylogeny. We summarize the known aspects concerning the choice of K and examine the results of using CVs with subtraction of a statistical background for K=3–9 and using raw CVs without subtraction for K=1–12. The criterion for evaluation consists in direct comparison with taxonomy. For prokaryotes the best performances are obtained for K=5 and 6 with subtraction and for K=11, 12 or even more without subtraction. In general, CVs with subtractions are slightly better and less CPU consuming, but CVs without subtraction may provide complementary information.
ISSN:1476-9271
1476-928X
DOI:10.1016/j.compbiolchem.2014.08.021