Premature terminator analysis sheds light on a hidden world of bacterial transcriptional attenuation
Université Paris-Sud, CNRS, UMR8621, Institut de Génétique et Microbiologie, Bâtiment 400, F-91405 Orsay Cedex, France
Genome Biology 2010, 11:R97 doi:10.1186/gb-2010-11-9-r97Published: 29 September 2010
Additional file 1:
Supplementary tables and figures. Table S0: gene families showing the highest absolute numbers of attenuator candidates. Table S1: genes most frequently regulated by attenuation in bacteria (normalized by family size). Table S2: list of sequence clusters observed in the 30 gene families most often regulated by attenuation (tabulation-separated). Table S3: sequence clusters obtained among candidates upstream of ABC-transporter genes. Table S4: complete list of clusters obtained by analyzing all candidates from enterobacterial species listed in Table S6. Cluster classes: 'a', clusters including only orthologous genes. 'b', clusters including only non-orthologous genes, sometimes from a single species; 'c', 'super-clusters' containing several sets of orthologous genes. Table S5: complete list of clusters obtained by analyzing all the candidates of Bacillus species listed in Table S6. 'a', clusters including only orthologous genes; 'b', clusters including only non-orthologous genes, sometimes from a single species; 'c', 'super-clusters' containing several sets of orthologous genes. Table S6: list of species analyzed for the identification of attenuators 'regulons'. Table S7: complete list of analyzed species, along with GenBank identifiers of corresponding DNA molecules and clade. Table S8: complete list of attenuators predicted in 5' UTR of genes, using the protocol described in  (tab-delimited table). Supplementary data 1: list of rimP-leaders from Gammaproteobacteria; list of rimP-leaders from other species; list of intergenic regions where no terminator could be detected, but showing sequence similarity to putative attenuators. Supplementary data 2: Stockholm alignments of the five ABC-leaders shown in Figure 4. Supplementary data 3: lists and Stockholm alignments of attenuator 'regulons' (candidates present upstream of several non-homologous genes) in Firmicutes. Supplementary data 4: parameters, commands and descriptor files used for terminator prediction.
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