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31:241-250. doi:10.1016/j.syapm.2008.07.001 [13] Ludwig W, Strunk O, Westram R, Richter L, Meier H, Yadhukumar A, Buchner T, Lai S, Steppi G, Jobb W, Forster I, Brettske S, Gerber AW, Ginhart O, Gross S, Grumann S, Hermann A, Vilbig M, Lenke T, Ludwig A. ARB: a software environment for sequence data. /Nucleic Acids Res/ 2004; 32:1363-1371. doi: 10.1093/nar/gkh293 [14] Stamatakis A. RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models. Bioinfo 2006; 22:2688. doi:10.1093/bioinformatics/btl446 [15] Field D, Garrity G, Gray T, Morrison N, Selengut J, Sterk P, Tatusova T, Thomson N, Allen MJ, Angiuoli SV. Towards a richer description of our complete collection of genomes and metagenomes: the “Minimum Information about a Genome Sequence” (MIGS) specification. Nat Biotechnol 2008; 26:541-547. doi:10.1038/nbt1360 [16] Euzéby JP. List of Bacterial Names with Standing in Nomenclature: a folder available on the Internet. Int J Syst Bacteriol 1997; 47:590-592. doi:10.1099/00207713-47-2-590 [17] Lilios K, Mavromatis K, Tavernarakis N, Kyrpides NC. The Genome On Line Database (GOLD) in 2007: Status of genomic and metagenomic projects and their associated metadata. Nuc Acids Res 2008; 36:475-479. doi:10.1093/nar/gkp848 [18] Zobell, C. E. 1941. Studies on marine bacteria. I. The cultural requirements of heterotrophic aerobes. J Mar Res 1941; 4:42-75. [19] Delcher AL, Bratke KA, Powers EC, Salzberg SL. Identifying bacterial genes and endosymbiont DNA with Glimmer. Bioinfo 2007; 23:673-679. doi:10.1093/bioinformatics/btm009 [20] Lowe TM, Eddy SR. tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence. Nuc Acids Res 1997; 25:955-964. PMID: 9023104 PMCID: PMC146525 [21] Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ. Basic local alignment search tool. J Mol Biol 1990; 215:403-410. doi:10.1016/S0022-2836(05)80360-2 [22] Meyer F, Goesmann A, McHardy AC, Bartels D, Bekel T, Clausen J, Kalinowski J, Linke B, Rupp O, Giegerich R, Puhler A. GenDB--an open source genome annotation system for prokaryote genomes. Nucl Acids Res 2003; 31:2187-2195. doi: 10.1093/nar/gkg312 [23] Emanuelsson O, Brunak S, Von Heijne G, Nielsen H. Locating proteins in the cell using TargetP, SignalP and related tools. Nat Protoc 2007; 2:953-971. doi:10.1038/nprot.2007.131 [24] Nielsen H, Brunak S, Von Heijne G. Machine learning approaches for the prediction of signal peptides and other protein sorting signals. Prot Eng 1999; 12:3- 9. PMID: 10065704 [25] Krogh A, Larsson B, Von Heijne G, Sonnhammer EL. Predicting transmembrane protein topology with a hidden Markov model: application to complete genomes. J Mol Biol S 2001; 305:567-580. doi:10.1006/jmbi.2000.4315 [26] Quast C. MicHanThi - design and implementation of a system for the prediction of gene functions in genome annotation projects. Master Thesis 2006 (Available on request). [27] Rutherford K, Parkhill J, Crook J, Horsnell T, Rice P, Rajandream MA, Barrell B. Artemis: sequence visualization and annotation. Bioinformatics 2000; 16:944-945. PMID: 11120685
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