Collins M, Brown J, Jones D. Brachybacterium faecium gen. nov., sp. nov., a coryneform bacterium from poultry deep litter. Int J Syst Bacteriol 1988; 38:45–48 doi:10.1099/00207713-38-1-45
Article
CAS
Google Scholar
Stackebrandt E, Rainey F, Ward-Rainey N. Proposal for a new hierarchic classification system, Actinobacteria classis nov. Int J Syst Bacteriol 1997; 47:479–491 doi:10.1099/00207713-47-2-479
Article
Google Scholar
Schefferle H. Coryneform bacteria in poultry deep litter. J Appl Bacteriol 1966; 29:147–160 doi:10.1111/j.1365-2672.1966.tb03462.x
Article
Google Scholar
Lee C, Grasso C, Sharlow MF. Multiple sequence alignment using partial order graphs. Bioinformatics 2002; 18:452–464 P-MID:11934745 doi:10.1093/bioinformatics/18.3.452
Article
CAS
PubMed
Google Scholar
Felsenstein J. Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 1981; 17:368–376 PMID:7288891 doi:10.1007/BF01734359
Article
CAS
PubMed
Google Scholar
Stamatakis A, Hoover P, Rougemont J. A rapid bootstrap algorithm for the RAxML Web servers. Syst Biol 2008; 57:758–771 PMID:18853362 doi:10.1080/10635150802429642
Article
PubMed
Google Scholar
Liolios K, Mavromatis K, Tavernarakis N, Kyrpides NC. The Genomes On Line Database (GOLD) in 2007: status of genomic and metagenomic projects and their associated metadata. Nucleic Acids Res 2008; 36:D475–479 PMID:17981842 doi:10.1093/nar/gkm884
Article
PubMed Central
CAS
PubMed
Google Scholar
Schleifer K, Lang K. Close relationship among strains of Micrococcus conglomeratus and Arthrobacter sp. FEMS Microbiol 1980; 9:223–226 doi:10.1111/j.1574-6968.1980.tb05641.x
Article
Google Scholar
Field D, Garrity G, Gray T, Morrison N, Selengut J, Sterk P, Tatusova T, Thomson N, Allen MJ, Angiuoli SV, et al. The minimum information about a genome sequence (MIGS) specification. Nat Biotechnol 2008; 26:541–547 PMID:18464787 doi:10.1038/nbt1360
Article
PubMed Central
CAS
PubMed
Google Scholar
Anonymous. Biological Agents: Technical rules for biological agents. <www.baua.de>.
Ashburner M, Ball CA, Blake JA, Botstein D, Butler H, Cherry JM, Davis AP, Dolinski K, Dwight SS, Eppig JT, et al. Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nat Genet 2000; 25:25–29 PMID:10802651 doi:10.1038/75556
Article
PubMed Central
CAS
PubMed
Google Scholar
Besemer J, Lomsadze A, Borodovsky M. GeneMarkS: a self-training method for prediction of gene starts in microbial genomes. Implications for finding sequence motifs in regulatory regions. Nucleic Acids Res 2001; 29:2607–2618 PMID:11410670 doi:10.1093/nar/29.12.2607
Article
PubMed Central
CAS
PubMed
Google Scholar
Markowitz V, Mavromatis K, Ivanova N, Chen I-M, Chu K, Palaniappan K, Szeto E, Anderson I, Lykidis A, Kyrpides N. Expert Review of Functional Annotations for Microbial Genomes. Bioinformatics 2009; in press.
Pati A. GenePRIMP: A Gene Prediction Improvement Pipeline for microbial genomes (In preparation 2009).
Lowe TM, Eddy SR. tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence. Nucleic Acids Res 1997; 25:955–964 PMID:9023104 doi:10.1093/nar/25.5.955
Article
PubMed Central
CAS
PubMed
Google Scholar
Lagesen K, Hallin P, Rodland EA, Staerfeldt HH, Rognes T, Ussery DW. RNAmmer: consistent and rapid annotation of ribosomal RNA genes. Nucleic Acids Res 2007; 35:3100–3108 PMID:17452365 doi:10.1093/nar/gkm160
Article
PubMed Central
CAS
PubMed
Google Scholar
Griffiths-Jones S, Moxon S, Marshall M, Khanna A, Eddy SR, Bateman A. Rfam: annotating non-coding RNAs in complete genomes. Nucleic Acids Res 2005; 33:D121–D124 PMID:15608160 doi:10.1093/nar/gki081
Article
PubMed Central
CAS
PubMed
Google Scholar
Markowitz VM, Szeto E, Palaniappan K, Grechkin Y, Chu K, Chen IM, Dubchak I, Anderson I, Lykidis A, Mavromatis K, et al. The integrated microbial genomes (IMG) system in 2007: data content and analysis tool extensions. Nucleic Acids Res 2008; 36:D528–D533 PMID:17933782 doi:10.1093/nar/gkm846
Article
PubMed Central
CAS
PubMed
Google Scholar
Karp P, Paley S, Romero P. The pathway tools software. Bioinformatics 2000; 18:S225–232
Article
Google Scholar
Caspi R, Foerster H, Fulcher CA, Kaipa P, Krummenacker M, Latendresse M, Paley S, Rhee SY, Shearer AG, Tissier C, et al. The MetaCyc Database of metabolic pathways and enzymes and the BioCyc collection of Pathway/Genome Databases. Nucleic Acids Res 2008; 36:D623–631 PMID:17965431 doi:10.1093/nar/gkm900
Article
PubMed Central
CAS
PubMed
Google Scholar
Karp PD, Ouzounis CA, Moore-Kochlacs C, Goldovsky L, Kaipa P, Ahren D, Tsoka S, Darzentas N, Kunin V, Lopez-Bigas N. Expansion of the BioCyc collection of pathway/genome databases to 160 genomes. Nucleic Acids Res 2005; 33:6083–6089 PMID:16246909 doi:10.1093/nar/gki892
Article
PubMed Central
CAS
PubMed
Google Scholar