Open Access Research article

Identification of candidate structured RNAs in the marine organism 'Candidatus Pelagibacter ubique'

Michelle M Meyer1, Tyler D Ames1, Daniel P Smith4, Zasha Weinberg3, Michael S Schwalbach4, Stephen J Giovannoni4 and Ronald R Breaker123*

Author Affiliations

1 Department of Molecular Cellular and Developmental Biology, Yale University, Box 208103, New Haven, CT 06520, USA

2 Department of Molecular Biophysics and Biochemistry, Yale University, Box 208103, New Haven, CT 06520, USA

3 Howard Hughes Medical Institute, Yale University, Box 208103, New Haven, CT 06520, USA

4 Department of Microbiology, Oregon State University, Corvallis, OR 97333, USA

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BMC Genomics 2009, 10:268  doi:10.1186/1471-2164-10-268

Published: 16 June 2009

Additional files

Additional file 1:

All 'Cand. P. ubique' IGRs greater than 100 bp. A list of all intergenic regions in 'Cand. P. ubique' longer than 100 bp with the length, GC content and annotated RNAs indicated.

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Additional file 2:

Misannotated protein coding regions identified. A list of likely misannotated protein coding regions identified in the course of this study.

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Additional file 3:

IGR ranking by %GC and sliding window %GC. Comparison of ranking IGRs by %GC and an alternative ranking methodology based on a sliding window of 50 nucleotides.

Format: DOC Size: 34KB Download file

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Additional file 4:

rpsB alignment. Text file containing Stockholm alignment of the rpsB motif, may be viewed in any text editor including XEmacs with the RALEE extension, or MS-wordpad.

Format: TXT Size: 373KB Download file

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Additional file 5:

rpsL alignment. Text file containing Stockholm alignment of the rpsL motif, may be viewed in any text editor including XEmacs with the RALEE extension, or MS-wordpad.

Format: TXT Size: 118KB Download file

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Additional file 6:

ffh alignment. Text file containing Stockholm alignment of the ffh motif, may be viewed in any text editor including XEmacs with the RALEE extension, or MS-wordpad.

Format: TXT Size: 109KB Download file

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Additional file 7:

SAMV alignment. Text file containing Stockholm alignment of the SAM-V motif, may be viewed in any text editor including XEmacs with the RALEE extension, or MS-wordpad.

Format: TXT Size: 74KB Download file

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Additional file 8:

rhtb alignment. Text file containing Stockholm alignment of the rhtb motif, may be viewed in any text editor including XEmacs with the RALEE extension, or MS-wordpad.

Format: TXT Size: 130KB Download file

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Additional file 9:

pntA alignment. Text file containing Stockholm alignment of the pntA motif, may be viewed in any text editor including XEmacs with the RALEE extension, or MS-wordpad.

Format: TXT Size: 39KB Download file

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Additional file 10:

bablM alignment. Text file containing Stockholm alignment of the bablM motif, may be viewed in any text editor including XEmacs with the RALEE extension, or MS-wordpad.

Format: TXT Size: 41KB Download file

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Additional file 11:

SAR11_0636 alignment. Text file containing Stockholm alignment of the SAR11_0636 motif, may be viewed in any text editor including XEmacs with the RALEE extension, or MS-wordpad.

Format: TXT Size: 65KB Download file

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Additional file 12:

RNA motifs from Alphaproteobacteria ordered by length. Glycine riboswitch, TPP riboswitch, SRP, and RNaseP RNAs from Alphaproteobacteria ordered by length.

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