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Open Access Highly Accessed Research article

Comparative analysis of structured RNAs in S. cerevisiae indicates a multitude of different functions

Stephan Steigele12, Wolfgang Huber3, Claudia Stocsits2, Peter F Stadler245 and Kay Nieselt1*

Author Affiliations

1 Wilhelm-Schickard-Institut für Informatik, ZBIT-Center for Bioinformatics Tübingen, University of Tübingen, Sand-14, D-72076 Tübingen, Germany

2 Bioinformatics Group, Department of Computer Science, and Interdisciplinary Center for Bioinformatics (IZBI), University of Leipzig, Härtelstraße 16-18, D-04107 Leipzig, Germany

3 EMBL Outstation Hinxton, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK

4 Department of Theoretical Chemistry University of Vienna, Währingerstraße 17, A-1090 Wien, Austria

5 Santa Fe Institute, 1399 Hyde Park Rd., Santa Fe, NM 87501, USA

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BMC Biology 2007, 5:25  doi:10.1186/1741-7007-5-25

Published: 18 June 2007

Additional files

Additional file 1:

Predicted RNA structures in fasta file format. The element_id is decomposed as follows: StartCoord_Length_Chr_strand. First part of the file contains RNA structure elements found on the PSVM0.5 and the second part RNA structure elements found on the PSVM0.9 cutoff level.

Format: FAST Size: 585KB Download file

Open Data

Additional file 2:

Distribution of z-scores of predicted structured RNA for each annotation class as reported by RNAz. (A) <a onClick="popup('http://www.biomedcentral.com/1741-7007/5/25/mathml/M1','MathML',630,470);return false;" target="_blank" href="http://www.biomedcentral.com/1741-7007/5/25/mathml/M1">View MathML</a> ≥ 0.5 (B) <a onClick="popup('http://www.biomedcentral.com/1741-7007/5/25/mathml/M1','MathML',630,470);return false;" target="_blank" href="http://www.biomedcentral.com/1741-7007/5/25/mathml/M1">View MathML</a> ≥ 0.9

Format: PDF Size: 1MB Download file

This file can be viewed with: Adobe Acrobat Reader

Open Data

Additional file 3:

Known RNA genes in the yeast genome, covered by predicted RNA structures. The annotation was taken from the Saccharomyces Genome Database. Structured elements with reported <a onClick="popup('http://www.biomedcentral.com/1741-7007/5/25/mathml/M1','MathML',630,470);return false;" target="_blank" href="http://www.biomedcentral.com/1741-7007/5/25/mathml/M1">View MathML</a> values larger than 0.5 and 0.9, respectively, are shown. SE denotes the sensitivity to detect functional classes of known RNAs, ali refers to the number of elements in the input alignments, mpi is the mean percent identity of the windows.

Format: PDF Size: 50KB Download file

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Open Data

Additional file 4:

Predicted RNA structures annotation file. The element_id is decomposed as follows: StartCoord_Length_Chr_strand. The first part of the file contains RNA structure elements found on the <a onClick="popup('http://www.biomedcentral.com/1741-7007/5/25/mathml/M1','MathML',630,470);return false;" target="_blank" href="http://www.biomedcentral.com/1741-7007/5/25/mathml/M1">View MathML</a> ≥ 0.5 and the second part RNA structure elements found on the <a onClick="popup('http://www.biomedcentral.com/1741-7007/5/25/mathml/M1','MathML',630,470);return false;" target="_blank" href="http://www.biomedcentral.com/1741-7007/5/25/mathml/M1">View MathML</a> ≥ 0.9 cut-off level. File isorganized as follows: element_id, strand of element on genome sequence, length of element, startcoord of overlap, endcoord of element, feature, feature name, strand of feature on genome sequence, length of feature, start coord of overlap, end coord of overlap.

Format: TXT Size: 413KB Download file

Open Data

Additional file 5:

CDS with conserved RNA structure. RNA structure found within CDS (<a onClick="popup('http://www.biomedcentral.com/1741-7007/5/25/mathml/M1','MathML',630,470);return false;" target="_blank" href="http://www.biomedcentral.com/1741-7007/5/25/mathml/M1">View MathML</a> ≥ 0.5 cut-off level). File is formatted as: CDS identifier, start of predicted structure, end of predicted structure, mean percent identity.

Format: TXT Size: 9KB Download file

Open Data

Additional file 6:

Predicted RNA structures in UTR regions. The element_id is decomposed as follows: StartCoord_Length_Chr_strand. The file contains all RNA structure elements found on the <a onClick="popup('http://www.biomedcentral.com/1741-7007/5/25/mathml/M1','MathML',630,470);return false;" target="_blank" href="http://www.biomedcentral.com/1741-7007/5/25/mathml/M1">View MathML</a> ≥ 0.5 cut-off level. File is formatted as element id, CDS with UTR, distance from CDS boundary, 5'/3' UTR.

Format: TXT Size: 5KB Download file

Open Data

Additional file 7:

Predicted structured RNA overlapping with TF-binding sites. Data is at the <a onClick="popup('http://www.biomedcentral.com/1741-7007/5/25/mathml/M1','MathML',630,470);return false;" target="_blank" href="http://www.biomedcentral.com/1741-7007/5/25/mathml/M1">View MathML</a> ≥ 0.5 cut-off level. File is formatted as: element id, SGD identifier for TF-binding site.

Format: TXT Size: 25KB Download file

Open Data

Additional file 8:

Structured RNAs providing evidence for snoRNAs. The scores are given as reported by snoSCAN for C/D-box snoRNAs and snoGPS for H/ACA snoRNAs. The score-cutoff, as reported by the indiviual predictions tools, was defined by analysis of all known snoRNAs from yeast. We used the minimal reported score as cutoff (1 stem snoGPS = 14; 2 stem snoGPS = 21; snoSCAN = 14). RNA elements that were positively predicted by both, the 1 and 2 stem scanner mode of snoGPS are given in bold type.

Format: PDF Size: 65KB Download file

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Open Data

Additional file 9:

Predicted RNA structures in intergenic regions. The element_id is decomposed as follows: StartCoord_Length_Chr_strand. The file contains all RNA structure elements found on the <a onClick="popup('http://www.biomedcentral.com/1741-7007/5/25/mathml/M1','MathML',630,470);return false;" target="_blank" href="http://www.biomedcentral.com/1741-7007/5/25/mathml/M1">View MathML</a> ≥ 0.5 cut-off level. File is formatted as intergenic RNA elements overlapping with data from David et al, Davis et al, Samanta et al and with SAGE/EST data.

Format: TXT Size: 15KB Download file

Open Data

Additional file 10:

Analysis of potential duplexes formed by predicted intergenic ncRNA transcripts. First, we filtered potential duplexes by fast searches for overlap regions with wublast (Gish, W., personal communication) with parameters that also allow for G-U basepairs, as described in Steigele et al [3]. Second, the thermodynamically preferred duplex between two predicted RNA molecules was calculated by RNAcofold. In most cases, only very large overlaps between predicted RNA molecules were found.

Format: PDF Size: 596KB Download file

This file can be viewed with: Adobe Acrobat Reader

Open Data