Identification of chromosomal alpha-proteobacterial small RNAs by comparative genome analysis and detection in Sinorhizobium meliloti strain 1021

doi:10.1186/1471-2164-8-467

BMC Genomics
Volume 8

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Research article

Identification of chromosomal alpha-proteobacterial small RNAs by comparative genome analysis and detection in Sinorhizobium meliloti strain 1021

Vincent M Ulvé^*¹ , Emeric W Sevin^*¹ , Angélique Chéron¹ and Frédérique Barloy-Hubler¹^,2

¹CNRS UMR6061 Génétique et Développement, Groupe Modèles Génétiques, Université de Rennes 1, IFR140 GFAS, Faculté de médecine, 2 avenue du Professeur Léon Bernard, CS 34317, 35043 Rennes Cedex, France

²CNRS UMR6026 Interactions Cellulaires et Moléculaires, Groupe DUALS, Université de Rennes 1, IFR140 GFAS, Campus de Beaulieu, avenue du Général Leclerc, 35042 Rennes, France

author email corresponding author email* Contributed equally

BMC Genomics 2007, 8:467doi:10.1186/1471-2164-8-467


Published:	19 December 2007

Additional files

Additional file 1:

Phylogenetic maximum likelihood trees of alpha-proteobacteria ffs, rnpB and tmRNA sequences. The data provided shows the phylogenetic maximum likelihood trees in subgroup-2 alpha-proteobacteria of the canonical tmRNA, rnpB and ffs small RNAs.

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Additional file 2:

BlastN detection of E. coli small genes in S. meliloti genome. The data provided describes the results of homology searches for E. coli small RNAs in the S. meliloti genome.

Format: PDF Size: 51KB Download file

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Additional file 3:

sRNAPredict outputs. The data provided presents the results obtained with sRNAPredict on S. meliloti's chromosome.

Format: PDF Size: 38KB Download file

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Additional file 10:

Short (FASTA) alignment and corresponding synteny results. The data provided shows the results of the search for small regions of homology between alpha-proteobacteria.

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Additional file 11:

Artemis Comparison Tool (ACT) screenshots alignment and corresponding synteny results. The data provided presents the results of the ACT comparisons.

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Additional file 4:

Intergenic regions included in this study. The data provided lists the intergenic regions selected (sra candidates) for in vivo validation and their features.

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Additional file 5:

Normalized expression levels (log₂SNR) of IGRs candidates. The data provided compiles the normalized expression levels for the candidates.

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Additional file 12:

TargetRNA results. The data provided shows the results of the target analysis for each valid sra gene.

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Additional file 13:

Alifold and RNAz secondary predictions. The data provided presents the alternative structures predicted for sra genes depending on the tools used.

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Additional file 6:

sra41 multiple loci in S. meliloti and related alpha-proteobacteria. The data provided features the multiple loci of sra41 in subgroup-2 alpha-proteobacteria.

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Additional file 7:

Strains used in this study.The data provided references the different bacteria used in this study.

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Additional file 8:

Oligonucleotides used in RACE and Northern assays. The data provided presents the oligonucleotide sequences used in RACE and Northern assays.

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Additional file 9:

Oligonucleotides used in microarray design. The data provided presents the oligonucleotide sequences used in the microarray design.

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