Research article
Identification of candidate structured RNAs in the marine organism 'Candidatus Pelagibacter ubique'
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* Corresponding author: Ronald R Breaker ronald.breaker@yale.edu
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
BMC Genomics 2009, 10:268 doi:10.1186/1471-2164-10-268
Published: 16 June 2009Additional 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
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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