RNA Structure
Local Sequence-Structure Alignment of RNA
In this project, we study the alignment of RNA using sequence and structure
information of the molecules. A special focus of the project is on local
alignment of RNAs.
The most recent outcome of the project is the tool LocARNA, which was already
successfully applied for genome-wide clustering of ncRNAs. In prior work, we
focussed on a specialized form of locality for RNAs, structural locality, and
developed the algorithm LSSA for local sequence structure alignment.
LocARNA is a tool for producing high-quality pairwise and multiple alignment of RNA sequences. It
uses a complex RNA energy model for simultaneous folding and sequence/structure alignment of the RNAs.
LocARNA performs global, sequence local, or even structurally local alignment of the molecules.
The tool LocARNA and the older LSSA are available for download
as source code from our Software page.
Contributing group members
Main Publications
Cooperations
- Kristin Reiche, University Leipzig
- Ivo Hofacker, TBI, University Vienna
- Peter Stadler, University Leipzig
Inverse RNA Folding
Here, we consider the inverse RNA folding problem, that means
designing RNA sequences that fold into a given structure.
We develop a new algorithm for the inverse folding problem (INFO-RNA)
that consists of two parts: a dynamic programming method for good initial
sequences and a following improved stochastic local search that uses an
effective neighbor selection method. During the initialization, we design a sequence that
among all sequences adopts the given structure with the lowest possible energy.
Software/Webserver: INFO-RNA
We present a free version of the source code of
INFO-RNA 1.0 and
INFO-RNA 2.0, which can be downloaded
here . Furthermore, you can
design your sequence online.
Contributing group members
Main Publications
- Anke Busch and Rolf Backofen (2007)
INFO-RNA - A Server for Fast Inverse RNA Folding Satisfying Sequence Constraints.
Nucleic Acid Research, 2007; 35(Web Server Issue):W310-3.
PDF(91 KB)
BibTeX Entry
- Anke Busch and Rolf Backofen (2006)
INFO-RNA - a fast approach to inverse RNA folding.
Bioinformatics, 2006; 22(15), 1823-31.
PDF(160 KB)
BibTeX Entry
Identifikation regulatorischer RNAs
Die stetig wachsende Anzahl von experimentell identifizierten regulatorischen
RNAs in Bakterien macht deutlich, dass RNAs eine entscheidende Rolle bei der
Regulation der Genexpression haben. Eine große Klasse dieser bakteriellen
regulatorischen RNAs bindet ihre Zielgene über Basenpaarung, wodurch sich die
Translationrate und/oder Stabilität der Zielgene ändert. Unsere Arbeitsgruppe
beschäftigt sich mit der Entwicklung von effizienten Algorithmen zur Vorhersage
von Interaktionen zwischen solchen regulatorischen RNAs und ihren Zielgenen. Die
von uns entwickelten Programme werden vorrangig zur genomweiten Vorhersage von
potenziellen Zielgenen in diversen Bakterienarten eingesetzt. Damit ermöglichen
wir eine funktionale Charakterisierung von neu identifizierten regulatorischen
RNAs in silico.
Contributing group members
Selenoproteins and Protein Design
Selenoproteins contain the 21th amino acid Selenocysteine, which is encoded by the STOP-codon UGA.
For its insertion it requires a specific mRNA sequence downstream the UGA-codon that forms a
hairpin-like structure (called Sec insertion sequence (SECIS)). Selenoproteins have gained much
interest recently since they are very important for human health. In contrast, very little is known
about selenoproteins. One reason for this is that one is not able to produce enough amount of
selenoproteins by using recombinant expression in a system like E.coli. The reason is that the
insertion mechanisms are different between E.coli and eukaryotes. Thus, one has to redesign the
human/mammalian selenoprotein for the expression in E.coli. Here, we developed an polynomial-time
algorithm for solving the computational problem involved in this design.
Webserver: SECISDesign
We present a server for the design of SECIS-elements and arbitrary RNA-elements within the coding sequence
of an mRNA. The element has to satisfy both structure and sequence constraints. At the same time, a certain
amino acid similarity to the original protein has to be kept. The designed sequence can be used for
recombinant expression of selenoproteins in Escherichia coli.
Contributing group members
Main Publications
- Anke Busch, Sebastian Will, and Rolf Backofen (2005)
SECISDesign: a server to design SECIS-elements within the coding sequence.
Bioinformatics, 21(15), 3312-3.
PDF (53KB)
BibTeX
Entry
- Rolf Backofen and Anke Busch (2004)
Computational Design of New and Recombinant Selenoproteins.
Proc. of the 15th Annual Symposium on Combinatorial Pattern Matching (CPM2004).
Postscript, gziped (175KB)
BibTeX Entry
Related Research Topics
Coarse Energy Landscape Representations for RNA Molecules
Based on the energy landscape library, a set of tools to investigate the
structure and topology of RNA energy landscapes has been implemented. These
programs allow for:
- Minima sampling
- Exact calculation of barrier trees or saddle networks
- Approximation of barrier trees
- Barrier estimation using a heuristic by Morgan and Higgs
Click here for further details
MARNA: Multiple Alignment of RNA
Multiple alignments of RNAs are an essential prerequisite to further
analyzes such as homology modelling, motif description or illustration
of conserved or variable binding sites. Beyond the comparison of RNAs
on the sequence level, structural conformations determined by
base-pairs have to be taken into account. Several pairwise
sequence-structure alignment methods have been developed. They use
extended alignment scores that evaluate secondary structure
information in addition to sequence information. However, two problems
for the multiple alignment step remain. First, how to combine pairwise
sequence-structure alignments into a multiple alignment and second,
how to generate secondary structure information for sequences whose
structural information is missing.
MARNA is an approach for multiple alignment of RNAs taking into
considerations both the primary sequences and the secondary
structures. It relies on the pairwise sequence-structure comparison
strategy by generating a set of weighted alignment edges. This set is
processed by a consistency-based multiple alignment method.
Additionally, MARNA extracts a consensus- sequence and structure from
this generated multiple alignment. MARNA can be accessed via the
MARNA webpage .
Contributing group members
Main Publications
- Sven Siebert and Rolf Backofen (2006)
MARNA: multiple alignment and consensus structure prediction of RNAs based on sequence structure comparisons
Bioinformatics.
BibTeX
Entry
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