EDGAR 2.0: an enhanced software platform for comparative gene content analyses

Nucleic Acids Research

Volumn 44, Issue W1, 2016, Pages W22-W28

  Blom, Jochen ^a   Kreis, Julian ^a   Spänig, Sebastian ^a   Juhre, Tobias ^a   Bertelli, Claire ^b,c   Ernst, Corinna ^d   Goesmann, Alexander ^a  

^a JUSTUS LIEBIG UNIVERSITY   (Germany)

^b LAUSANNE UNIVERSITY HOSPITAL   (Switzerland)

^c SWISS INSTITUTE OF BIOINFORMATICS   (Switzerland)

^d UNIVERSITY HOSPITAL OF COLOGNE   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

ACCESS TO INFORMATION; ARTICLE; CALCULATION; CONTENT ANALYSIS; GENOME ANALYSIS; GENOME SIZE; INFORMATION PROCESSING; INFORMATION RETRIEVAL; MATHEMATICAL ANALYSIS; MYCOBACTERIUM; MYCOBACTERIUM TUBERCULOSIS; NONHUMAN; PHYLOGENY; SOFTWARE; XANTHOMONAS; BIOLOGY; COMPARATIVE STUDY; CONSERVED SEQUENCE; GENETIC DATABASE; GENETICS; INTERNET; MICROBIAL CONSORTIUM; PROCEDURES; SPECIES DIFFERENCE; STATISTICS AND NUMERICAL DATA; SYNTENY;

COMPUTATIONAL BIOLOGY; CONSERVED SEQUENCE; DATABASES, GENETIC; DATASETS AS TOPIC; INTERNET; MICROBIAL CONSORTIA; PHYLOGENY; SOFTWARE; SPECIES SPECIFICITY; SYNTENY;

EID: 84979250492     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/NAR/GKW255     Document Type: Article

References (31)

1. Tettelin,H., Masignani,V., Cieslewicz,M., Donati,C., Medini,D., Ward,N., Angiuoli,S., Crabtree,J., Jones,A., Durkin,A. et al. (2005) Genome analysis of multiple pathogenic isolates of Streptococcus agalactiae: implications for the microbial “pan-genome”. Proc. Natl. Acad. Sci. U.S.A., 102, 13950-13955.
2. Medini,D., Donati,C., Tettelin,H., Masignani,V. and Rappuoli,R. (2005) The microbial pan-genome. Curr. Opin. Genet. Dev., 15, 589-594.
3. Markowitz,V.M., Chen,I.-M.A., Palaniappan,K., Chu,K., Szeto,E., Grechkin,Y., Ratner,A., Jacob,B., Huang,J., Williams,P. et al. (2012) IMG: the integrated microbial genomes database and comparative analysis system. Nucleic Acids Res., 40, D115-D122.
4. Dehal,P.S., Joachimiak,M.P., Price,M.N., Bates,J.T., Baumohl,J.K., Chivian,D., Friedland,G.D., Huang,K.H., Keller,K., Novichkov,P.S. et al. (2010) MicrobesOnline: an integrated portal for comparative and functional genomics. Nucleic Acids Res., 38, D396-D400.
5. Uchiyama,I., Mihara,M., Nishide,H. and Chiba,H. (2013) MBGD update 2013: the microbial genome database for exploring the diversity of microbial world. Nucleic Acids Res., 41, D631-D635.
6. Whiteside,M.D., Winsor,G.L., Laird,M.R. and Brinkman,F.S. (2013) OrtholugeDB: a bacterial and archaeal orthology resource for improved comparative genomic analysis. Nucleic Acids Res., 41, D366-D376.
7. Blom,J., Albaum,S.P., Doppmeier,D., Pühler,A., Vorhölter,F.-J., Zakrzewski,M. and Goesmann,A. (2009) EDGAR: a software framework for the comparative analysis of prokaryotic genomes. BMC Bioinformatics, 10, 154.
8. R Development Core Team. (2008) R: a language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, ISBN 3-900051-07-0.
9. Lerat,E., Daubin,V. and Moran,N. (2003) From gene trees to organismal phylogeny in prokaryotes: the case of the gamma-Proteobacteria. PLoS Biol., 1, 101-109.
10. Tettelin,H., Riley,D., Cattuto,C. and Medini,D. (2008) Comparative genomics: the bacterial pan-genome. Curr. Opin. Microbiol., 11, 472-477.
11. Zdobnov,E. and Bork,P. (2007) Quantification of insect genome divergence. Trends Genet., 23, 16-20.
12. Edgar,R. (2004) MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res., 32, 1792-1797.
13. Felsenstein,J. (1989) PHYLIP-phylogeny inference package (version 3.2). Cladistics, 5, 163-166.
14. Konstantinidis,K.T. and Tiedje,J.M. (2005) Towards a genome-based taxonomy for prokaryotes. J. Bacteriol., 187, 6258-6264.
15. Konstantinidis,K.T. and Tiedje,J.M. (2005) Genomic insights that advance the species definition for prokaryotes. Proc. Natl. Acad. Sci. U.S.A., 102, 2567-2572.
16. Konstantinidis,K.T., Ramette,A. and Tiedje,J.M. (2006) The bacterial species definition in the genomic era. Philos. Trans. R. Soc. Lond B Biol. Sci., 361, 1929-1940.
17. Altschul,S.F., Gish,W., Miller,W., Myers,E.W. and Lipman,D.J. (1990) Basic local alignment search tool. J. Mol. Biol., 215, 403-410.
18. Goris,J., Konstantinidis,K.T., Klappenbach,J.A., Coenye,T., Vandamme,P. and Tiedje,J.M. (2007) DNA-DNA hybridization values and their relationship to whole-genome sequence similarities. Int. J. Syst. Evol. Microbiol., 57, 81-91.
19. Richter,M. and Rosselló-Móra,R. (2009) Shifting the genomic gold standard for the prokaryotic species definition. Proc. Natl. Acad. Sci. U.S.A., 106, 19126-19131.
20. Pribnow,D. (1975) Nucleotide sequence of an RNA polymerase binding site at an early T7 promoter. Proc. Natl. Acad. Sci. U.S.A., 72, 784-788.
21. Hain,T., Hossain,H., Chatterjee,S.S., Machata,S., Volk,U., Wagner,S., Brors,B., Haas,S., Kuenne,C.T., Billion,A. et al. (2008) Temporal transcriptomic analysis of the Listeria monocytogenes EGD-e regulon. BMC Microbiol., 8, 1-12.
22. Morgan,H.P., Estibeiro,P., Wear,M.A., Max,K.E., Heinemann,U., Cubeddu,L., Gallagher,M.P., Sadler,P.J. and Walkinshaw,M.D. (2007) Sequence specificity of single-stranded DNA-binding proteins: a novel DNA microarray approach. Nucleic Acids Res., 35, e75.
23. Kuenne,C., Ghai,R., Chakraborty,T. and Hain,T. (2007) GECO-linear visualization for comparative genomics. Bioinformatics, 23, 125-126.
24. Rice,P., Longden,I., Bleasby,A. et al. (2000) EMBOSS: the European molecular biology open software suite. Trends Genet., 16, 276-277.
25. Eddy,S.R. (1996) Hidden markov models. Curr. Opin. Struct. Biol., 6, 361-365.
26. Eddy,S. (2011) Accelerated profile HMM searches. PLoS Comput. Biol., 7, e1002195.
27. Borriss,R., Chen,X.-H., Rueckert,C., Blom,J., Becker,A., Baumgarth,B., Fan,B., Pukall,R., Schumann,P., Spröer,C. et al. (2011) Relationship of Bacillus amyloliquefaciens clades associated with strains DSM 7T and FZB42T: a proposal for Bacillus amyloliquefaciens subsp. amyloliquefaciens subsp. nov. and Bacillus amyloliquefaciens subsp. plantarum subsp. nov. based on complete genome sequence comparisons. Int. J. Syst. Evol. Microbiol., 61, 1786-1801.
28. Sangal,V., Blom,J., Sutcliffe,I.C., von Hunolstein,C., Burkovski,A. and Hoskisson,P.A. (2015) Adherence and invasive properties of Corynebacterium diphtheriae strains correlates with the predicted membrane-associated and secreted proteome. BMC Genomics, 16, 1-15.
29. Glaeser,S.P., Imani,J., Alabid,I., Guo,H., Kumar,N., Kämpfer,P., Hardt,M., Blom,J., Goesmann,A., Rothballer,M. et al. (2015) Non-pathogenic Rhizobium radiobacter F4 deploys plant beneficial activity independent of its host Piriformospora indica. ISME J., 10, 871-884.
30. Ngugi,D.K., Blom,J., Stepanauskas,R. and Stingl,U. (2015) Diversification and niche adaptations of Nitrospina-like bacteria in the polyextreme interfaces of Red Sea brines. ISME J., doi:10.1038/ismej.2015.214.
31. Mann,R., Blom,J., Bühlmann,A., Plummer,K., Beer,S., Luck,J., Goesmann,A., Frey,J., Rodoni,B., Duffy,B. et al. (2012) Comparative analysis of the Hrp pathogenicity island of Rubus- and Spiraeoideae-infecting Erwinia amylovora strains identifies the IT region as a remnant of an integrative conjugative element. Gene, 504, 6-12.