(PDF 20 KB) Additional file 6: Distribution of the BLAST Bit Score (BSR) for several paired comparisons. The genes of Xeu8 were used as reference to build histograms of BSR values here displayed in logarithmic scale (blue). In purple, is the distribution by larger windows of values. In green,
is the automatically selected threshold based on the valley of the distribution. Discontinuous purple shows the average threshold, while grey indicates four extreme points of the Vorinostat distribution used to evaluate its topology. (PDF 70 KB) Additional file 7: Supplementary methods. A supplementary text describing methods for the construction of OGs using the Bit Score Ratio with static (BSR-Manual) and dynamic thresholds (BSR-Auto), and the BLAST
Reciprocal Androgen Receptor activity inhibition Best Match (RBM). (PDF 85 KB) References 1. Hayward AC: The host of Xanthomonas . In Xanthomonas. Edited by: Swings J-G, Civerolo EL. London: Chapman & Hall; 1993:52–54. 2. Egel DS, Graham JH, Stall RE: Genomic relatedness of Xanthomonas campestris strains causing diseases of Citrus . Appl Environ Microbiol 1991, 57:2724–2730.PubMed 3. Louws FJ, Fulbright DW, Stephens CT, de Bruijn FJ: Specific genomic fingerprints of phytopathogenic Xanthomonas and Pseudomonas pathovars and strains generated with repetitive sequences and PCR. Appl Environ Microbiol 1994, 60:2286–2295.PubMed 4. Rademaker JLW, Hoste B, Louws FJ, et al.: Comparison of AFLP and rep-PCR genomic fingerprinting with DNA-DNA homology studies: Xanthomonas as a model
system. Int J Syst Evol Microbiol 2000, 50:665–677.PubMedCrossRef 5. Simões THN, Gonçalves ER, Rosato YB, Mehta A: Differentiation of Xanthomonas AG-881 purchase species by PCR-RFLP of rpfB and atpD genes. FEMS Microbiol Lett 2007, 271:33–39.PubMedCrossRef 6. Vauterin L, Hoste B, Kersters K, Swings J: Reclassification of Xanthomonas . Int J Syst Evol Microbiol 1995, 45:472. 7. Parkinson NM, Aritua V, Heeney J, et al.: Phylogenetic analysis of Xanthomonas species by comparison of partial gyrase B gene sequences. Int J Syst Evol Microbiol 2007, 57:2881–2887.PubMedCrossRef BCKDHA 8. Koebnik R: The Xanthomonas Resource. [http://www.xanthomonas.org/] 9. Ryan RP, Vorhölter F-J, Potnis N, et al.: Pathogenomics of Xanthomonas : understanding bacterium-plant interactions. Nature reviews. Microbiology 2011, 9:344–355.PubMed 10. Blom J, Albaum SP, Doppmeier D, et al.: EDGAR: a software framework for the comparative analysis of prokaryotic genomes. BMC Bioinforma 2009, 10:154.CrossRef 11. Moreira LM, Almeida NF, Potnis N, et al.: Novel insights into the genomic basis of citrus canker based on the genome sequences of two strains of Xanthomonas fuscans subsp. aurantifolii . BMC Genomics 2010, 11:238.PubMedCrossRef 12. Doidge EM: A tomato canker. Ann Appl Biol 1921, 7:407–430.CrossRef 13. Dowson WJ: On the systematic position and generic names of the gram negative bacterial plant pathogens.