SNP-associations and phenotype predictions from hundreds of microbial genomes without genome alignments

PLoS ONE

Volumn 9, Issue 2, 2014, Pages

  Hall, Barry G ^a  

^a Bellingham Research Institute   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ACCURACY; ARTICLE; BACTERIAL GENOME; BACTERIAL STRAIN; CONTROLLED STUDY; ESCHERICHIA COLI; GENE IDENTIFICATION; GENE SEQUENCE; GENETIC ASSOCIATION; GENETIC DATABASE; NONHUMAN; NUCLEOTIDE SEQUENCE; PATHOGENICITY; PHENOTYPE; PREDICTION; SEQUENCE ALIGNMENT; SHIGELLA; SINGLE NUCLEOTIDE POLYMORPHISM; BIOLOGY; CLASSIFICATION; COMPUTER PROGRAM; GENETICS; MICROBIAL GENOME; PHYLOGENY; PROCEDURES; REPRODUCIBILITY;

COMPUTATIONAL BIOLOGY; ESCHERICHIA COLI; GENOME, BACTERIAL; GENOME, MICROBIAL; PHENOTYPE; PHYLOGENY; POLYMORPHISM, SINGLE NUCLEOTIDE; REPRODUCIBILITY OF RESULTS; SHIGELLA; SOFTWARE;

EID: 84896520688     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0090490     Document Type: Article

References (10)

1. Gardner SN, Slezak T (2010) Scalable SNP analyses of 100+ bacterial or viral genomes. J Forensic Science 1: 107-111.
2. Gardner SN, Hall BG (2013) When whole-genome alignments just won't work: kSNP v2 software for alignment-free SNP discovery and phylogenetics of hundreds of microbial genomes. PLoS One 8.
3. Tamura K, Peterson D, Peterson N, Stecher G, Nei M, et al. (2011) MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Mol Biol Evol 28: 2731-2739.
4. Hall BG (2011) Phylogenetic Trees Made Easy: A How-To Manual, Fourth Edition. Sunderland, MA: Sinauer Assoc.
5. Hall BG (2013) Building Phylogenetic Trees from Molecular Data with MEGA. Mol Biol Evol 30: 1229-1235.
6. Nye TM, Lio P, Gilks WR (2006) A novel algorithm and web-based tool for comparing two alternative phylogenetic trees. Bioinformatics 22: 117-119. (Pubitemid 43057018)
7. Moore JH, Gilbert JC, Tsai CT, Chiang FT, Holden T, et al. (2006) A flexible computational framework for detecting, characterizing, and interpreting statistical patterns of epistasis in genetic studies of human disease susceptibility. J Theor Biol 241: 252-261. (Pubitemid 43993963)
8. Moore JH (2006) Epistasis Blog. http://compgen.blogspot.com/2006-11-01- archive.html
9. Sinclair RG, Rose JB, Hashsham SA, Gerba CP, Haas CN (2012) Criteria for selection of surrogates used to study the fate and control of pathogens in the environment. Appl Environ Microbiol 78: 1969-1977.
10. Luo C, Walk ST, Gordon DM, Feldgarden M, Tiedje JM, et al. (2011) Genome sequencing of environmental Escherichia coli expands understanding of the ecology and speciation of the model bacterial species. Proc Natl Acad Sci U S A 108: 7200-7205.