Research
Comparative genomics reveals 104 candidate structured RNAs from bacteria, archaea, and their metagenomes
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* Corresponding authors: Zasha Weinberg zasha.weinberg@yale.edu - Ronald R Breaker ronald.breaker@yale.edu
1 Howard Hughes Medical Institute, Yale University, P.O. Box 208103, New Haven, CT 06520-8103, USA
2 Department of Molecular, Cellular and Developmental Biology, Yale University, P.O. Box 208103, New Haven, CT 06520-8103, USA
3 Department of Molecular Biophysics and Biochemistry, Yale University, P.O. Box 208103, New Haven, CT 06520-8103, USA
4 Current address: Department of Biology, University of Rochester, Rochester, NY 14627, USA
5 Current address: School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
Genome Biology 2010, 11:R31 doi:10.1186/gb-2010-11-3-r31
Published: 15 March 2010Additional files
Additional file 1:
Supplementary results and discussion. Additional analysis of motifs, including those not discussed in the manuscript, and in-line probing experiments on riboswitch candidates.
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Additional file 2:
Summary and evaluation of all motifs. Table 1, with summary of supporting evidence, and numbers of representatives of each motif.
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Additional file 3:
Taxa of motif representatives, genes flanking representatives and annotated multiple-sequence alignments. For each motif, this file shows the taxa of each motif representative, depicts genes flanking these representatives and describes conserved domains that the genes encode. Also, a multiple-sequence alignment is provided for each motif, and includes secondary structure and other annotations.
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Additional file 4:
Raw text alignment files, including annotation. Raw alignments of RNAs, including annotations (for example, predicted transcription terminators, flanking sequences) in "Stockholm" text format. The alignment format and appropriate viewing programs are discussed on Wikipedia [113]. The Stockholm files can be retrieved from the .tar.gz archive file by using programs such as WinZip (Windows), StuffIt Expander (Mac), or tar/gzip (UNIX).
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Additional file 5:
Raw text alignment files, just the motifs. Raw alignments of RNA motifs with minimal annotation and no flanking sequences, in "Stockholm" text format. The Stockholm files can be retrieved from the .tar.gz archive file by using programs such as WinZip (Windows), StuffIt Expander (Mac), or tar/gzip (UNIX).
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Additional file 6:
Consensus diagrams of all motifs. Consensus diagrams depicting all motifs in high resolution.
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Additional file 7:
Alignment of YjdF proteins. Multiple-sequence alignment of proteins predicted to be homologous to YjdF of Bacillus subtilis.
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Additional file 8:
Genes associated with ykkC, mini-ykkC and ykkC-III RNAs. The frequencies with which various gene families are associated with ykkC, mini-ykkC or ykkC-III RNAs are listed.
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Additional file 9:
Partitioning of genomes and metagenomes. Describes how genomes and metagenomes were divided into pipeline runs.
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Additional file 10:
Source code implemented as part of this project. Source code files and a README.pdf file are provided to assist in detailed understanding of the methods. The files can be retrieved from the .tar.gz archive file, as described for Additional file 4.
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Additional file 11:
Overlap with previous raw predictions. Overlaps of our RNA motifs with raw predictions of a prior study [9]. Tab-delimited text file.
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