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Evaluation of thresholds for the detection of binding sites for regulatory proteins in Escherichia coli K12 DNA

Esperanza Benítez-Bellón, Gabriel Moreno-Hagelsieb* and Julio Collado-Vides*

Genome Biology 2002, 3:research0013-research0013.16 doi:10.1186/gb-2002-3-3-research0013

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Identifying promoter features of co-regulated genes with similar network motifs

Oscar Harari, Coral del Val, Rocío Romero-Zaliz, Dongwoo Shin, Henry Huang, Eduardo A Groisman, Igor Zwir BMC Bioinformatics 2009, 10(Suppl 4):S1 (29 April 2009)

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Research   Open Access

The mosaic structure of the symbiotic plasmid of Rhizobium etli CFN42 and its relation to other symbiotic genome compartments

Víctor González, Patricia Bustos, Miguel A Ramírez-Romero, Arturo Medrano-Soto, Heladia Salgado, Ismael Hernández-González, Juan Hernández-Celis, Verónica Quintero, Gabriel Moreno-Hagelsieb, Lourdes Girard, Oscar Rodríguez, Margarita Flores, Miguel A Cevallos, Julio Collado-Vides, David Romero, Guillermo Dávila Genome Biology 2003, 4:R36 (13 May 2003)

Abstract | Full text | PDF | PubMed | Cited on BioMed Central |  Editor’s summary

In rhizobia, essential genes for symbiosis are compartmentalized in symbiotic plasmids or in chromosomal symbiotic islands. The complete sequence of the symbiotic plasmid of Rhizobium etli CFN42, a microsymbiont of beans is reported, along with and a comparison with other symbiotic genome compartments sequences available.

Research   Open Access

Prediction and overview of the RpoN-regulon in closely related species of the Rhizobiales

Bruno Dombrecht, Kathleen Marchal, Jos Vanderleyden, Jan Michiels Genome Biology 2002, 3:research0076-research0076.11 (26 November 2002)

Abstract | Full text | PDF | PubMed | Cited on BioMed Central |  Editor’s summary

Two complete rhizobial genomes (Mesorhizobium loti, Sinorhizobium meliloti) and four symbiotic regions (Rhizobium etli, Rhizobium sp. NGR234, Bradyrhizobium japonicum, M. loti) were screened for the presence of highly conserved RpoN-binding sites. The methodology used to predict RpoN-binding sites proved highly effective as nearly all known RpoN-controlled genes were identified.

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