A new vector for identification of prokaryotes and their variable-size genomes

Current Microbiology

Volumn 66, Issue 1, 2013, Pages 96-101

  Hou, Tao ^a   Liu, Fu ^a   Lin, Caixia X ^b   Li, Dingyuan Y ^a  

^a JILIN UNIVERSITY   (China)

^b HAINAN UNIVERSITY   (China)

Author keywords

[No Author keywords available]

Indexed keywords

ACCURACY; ALGORITHM; ARTICLE; DNA BARCODING; FILTER; FILTRATION; GENE VECTOR; GENETIC VARIABILITY; GENOME ANALYSIS; GENOME SIZE; GENOMIC FRAGMENT; HORIZONTAL GENE TRANSFER; NUCLEOTIDE SEQUENCE; PHYLOGENY; PRIORITY JOURNAL; PROKARYOTE;

BACTERIA; COMPUTATIONAL BIOLOGY; GENETICS, MICROBIAL; GENOME, BACTERIAL; MOLECULAR BIOLOGY;

PROKARYOTA;

EID: 84871621421     PISSN: 03438651     EISSN: 14320991     Source Type: Journal    
DOI: 10.1007/s00284-012-0246-9     Document Type: Article

References (19)

1. Cole JR, Chai B, Marsh TL et al (2003) The Ribosomal Database Project (RDP-II): previewing a new auto aligner that allows regular updates and the new prokaryote taxonomy. Nucleic Acids Res 31:442-443
2. Cover T, Hart P (1967) Nearest neighbor pattern classification. IEEE Trans 13:21-27
3. Diaz NN, Krause L, Goesmann A et al (2009) TACOA: taxonomic classification of environmental genomic fragments using a kernelized nearest neighbor approach. BMC Bioinformatics 10:56
4. Godfray HCJ (2002) Challenges for taxonomy. Nature 417:17-19
5. Holt JG, Krieg NR, Sneath PHA (1997) Bergey's manual of determinative bacteriology. Williams & Wilkins, Baltimore
6. Karlin S, Brocchieri L, Mrazek J et al (1999) A chimeric prokaryotic ancestry of mitochondria and primitive eukaryotes. Proc Natl Acad Sci USA 96:9190-9195
7. Karlin S, Burge C (1995) Dinucleotide relative abundance extremes: a genomic signature. Trends Genet 11:283-290
8. Karlin S, Mrazek J, Ma J et al (2005) Predicted highly expressed genes in archaeal genomes. Proc Natl Acad Sci USA 102:7303-7308
9. Karlin S, Zhu ZY, Karlin KD (1997) The extended environment of mononuclear metal centers in protein structures. Proc Natl Acad Sci USA 94:14225-14230
10. McHardy AC, Martin HG, Tsirigos A et al (2007) Accurate phylogenetic classification of variable-length DNA fragments. Nat Methods 4:63-72
11. Mrazek J, Bhaya D, Grossman AR et al (2001) Highly expressed and alien genes of the Synechocystis genome. Nucleic Acids Res 29:1590-1601
12. Mrazek J, Karlin S (1999) Detecting alien genes in bacterial genomes. Ann N Y Acad Sci 870:314-329
13. Olsen GJ, Woese CR (1994) The winds of (evolutionary) change: breathing new life into microbiology. J Bacteriol 176:1-6
14. Otsu N (1979) A threshold selection method from Gray-level Histogram. IEEE Trans Syst Man Cybern SMC 9:62-66
15. Qi J, Luo H, Hao BL (2004) CVTree: a phylogenetic tree reconstruction tool based on whole genomes. Nucleic Acids Res 32:45-47
16. Qi J, Wang B, Hao BL (2004) Whole proteome prokaryote phylogeny without sequence alignment: a K-string composition approach. J Mol Evol 58:1-11
17. Woese CR, Fox GE (1977) Phylogenetic structure of the prokaryotic domain: the primary kingdoms. Proc Natl Acad Sci USA 74:5088-5090
18. Yao Z, Ruzzo WL (2006) A regression-based K nearest neighbor algorithm for gene functions prediction from heterogeneous data. BMC Bioinformatics 7(Suppl 1):S11
19. Zhou FF, Olman V, Xu Y (2008) Barcodes for genomes and applications. BMC Bioinformatics 9:546