title: On K-peptide length in composition vector phylogeny of prokaryotes.
abstract: 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.
authors.affiliation: T-Life Research Center, Fudan University, Shanghai 200433, China.
authors.forename: Guanghong
authors.initials: G
authors.lastname: Zuo
authors.affiliation: CAS-MPG Partner Institute for Computational Biology, Shanghai 200032, China.
authors.forename: Qiang
authors.initials: Q
authors.lastname: Li
authors.affiliation: T-Life Research Center, Fudan University, Shanghai 200433, China. Electronic address: hao@mail.itp.ac.cn.
authors.forename: Bailin
authors.initials: B
authors.lastname: Hao
mesh_terms: D000465:Algorithms; D001105:Archaea / Q000145:classification* / Q000235:genetics; D019843:Archaeal Proteins / Q000737:chemistry / Q000235:genetics; D001419:Bacteria / Q000145:classification* / Q000235:genetics; D001426:Bacterial Proteins / Q000737:chemistry / Q000235:genetics; D020745:Genome, Archaeal; D016680:Genome, Bacterial; D010455:Peptides / Q000737:chemistry / Q000235:genetics; D010802:Phylogeny; D017422:Sequence Analysis, DNA; D020539:Sequence Analysis, Protein
chemical_list: D019843:Archaeal Proteins; D001426:Bacterial Proteins; D010455:Peptides
keywords: Alignment-free; Composition vector; Prokaryote phylogeny and taxonomy; Subtraction procedure; Whole-genome-based