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

doi:10.1186/1471-2164-10-268

BMC Genomics

Volume 10

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Ames TD
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Weinberg Z
Schwalbach MS
Giovannoni SJ
Breaker RR

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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 Breaker¹^,2^,3

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

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

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

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

author email corresponding author email

BMC Genomics 2009, 10:268doi: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.

Format: DOC Size: 38KB Download file

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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

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

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

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

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

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

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

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

Additional file 12:

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

Format: DOC Size: 265KB Download file

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