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RNAalifold: improved consensus structure prediction for RNA alignments
The accuracy of RNAalifold predictions can be improved substantially by introducing a different, more rational handling of alignment gaps, and by replacing the rather simplistic model of covariance scoring with more sophisticated RIBOSUM-like scoring matrices.
Identification of Functional Elements and Regulatory Circuits by Drosophila modENCODE
Two studies identified regions of the nematode and fly genomes that show highly occupied targets (or HOT) regions where DNA was bound by more than 15 of the transcription factors analyzed and the expression of related genes were characterized.
Inferring Noncoding RNA Families and Classes by Means of Genome-Scale Structure-Based Clustering
A structure-based clustering approach that is capable of extracting putative RNA classes from genome-wide surveys for structured RNAs and suggests several novel classes of ncRNAs for which to date no representative has been experimentally characterized.
Freiburg RNA Tools: a web server integrating IntaRNA, ExpaRNA and LocARNA
- Cameron Smith, Steffen Heyne, Andreas S. Richter, S. Will, R. Backofen
- BiologyNucleic Acids Res.
- 5 May 2010
The Freiburg RNA tools web server integrates three tools for the advanced analysis of RNA in a common web-based user interface that support the prediction of RNA–RNA interaction, exact RNA matching and alignment of RNA, respectively.
LocARNA-P: accurate boundary prediction and improved detection of structural RNAs.
The ready-to-use software tool LocARNA-P produces structure-based multiple RNA alignments with associated columnwise STARs and predicts ncRNA boundaries and allows much stronger discrimination between true- and false-positive predictions than RNAz's own evaluation.
Excluding Symmetries in Constraint-Based Search
This work introduces a new method, called symmetry excluding search (SES), for excluding symmetries in constraint based search, which is the first declarative method that can be applied to arbitrary asymmetries, and proves correctness, completeness and symmetry exclusion properties.
CRISPRmap: an automated classification of repeat conservation in prokaryotic adaptive immune systems
- Sita Lange, O. Alkhnbashi, Dominic Rose, S. Will, R. Backofen
- BiologyNucleic acids research
- 17 July 2013
The largest data set of CRISPRs to date is compiled, comprehensive, independent clustering analyses are performed and a novel set of 40 conserved sequence families and 33 potential structure motifs for Cas-endoribonucleases with some distinct conservation patterns are identified.
Metallic and Insulating Phases of Repulsively Interacting Fermions in a 3D Optical Lattice
This work was able to directly measure the compressibility of the quantum gas in the trap using in situ imaging and independent control of external confinement and lattice depth, to demonstrate the potential to model interacting condensed-matter systems using ultracold fermionic atoms.
Variations on RNA folding and alignment: lessons from Benasque
A series of variations on standard methods that implement refined biophysical models, such as a restriction of RNA folding to canonical structures, and an extension of structural alignments to an explicit scoring of stacking propensities are discussed.
Ultracold Dipolar Gas of Fermionic 23Na40 K Molecules in Their Absolute Ground State.
We report on the creation of an ultracold dipolar gas of fermionic 23Na40 K molecules in their absolute rovibrational and hyperfine ground state. Starting from weakly bound Feshbach molecules, we…