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

doi:10.1186/1741-7007-5-25

BMC Biology

Volume 5

Viewing options:

Abstract
Full text
PDF (1MB)
Additional files

Associated material:

Related literature:

Articles citing this article
on BioMed Central
on Google Scholar
on ISI Web of Science
on PubMed Central
Other articles by authors
on Google Scholar

Steigele S
Huber W
Stocsits C
Stadler PF
Nieselt K

on PubMed

Steigele S
Huber W
Stocsits C
Stadler PF
Nieselt K
Related articles/pages
on Google

on Google Scholar

on PubMed

Tools:

Post to:

Research article

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

Stephan Steigele¹^,2 , Wolfgang Huber³ , Claudia Stocsits² , Peter F Stadler²^,4^,5 and Kay Nieselt¹

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

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

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

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

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

author email corresponding author email

BMC Biology 2007, 5:25doi: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 P_SVM^0.5and the second part RNA structure elements found on the P_SVM^0.9cutoff level.

Format: FAST Size: 585KB Download file

Additional file 2:

Distribution of z-scores of predicted structured RNA for each annotation class as reported by RNAz. (A) ≥ 0.5 (B) ≥ 0.9

Format: PDF Size: 1MB Download file

This file can be viewed with: Adobe Acrobat Reader

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 values larger than 0.5 and 0.9, respectively, are shown. S_Edenotes 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

This file can be viewed with: Adobe Acrobat Reader

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 ≥ 0.5 and the second part RNA structure elements found on the ≥ 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

Additional file 5:

CDS with conserved RNA structure. RNA structure found within CDS ( ≥ 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

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 ≥ 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

Additional file 7:

Predicted structured RNA overlapping with TF-binding sites. Data is at the ≥ 0.5 cut-off level. File is formatted as: element id, SGD identifier for TF-binding site.

Format: TXT Size: 25KB Download file

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

This file can be viewed with: Adobe Acrobat Reader

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 ≥ 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

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