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An updated evolutionary classification of CRISPR–Cas systems
An approach combining the analysis of signature protein families and features of the architecture of cas loci that unambiguously partitions most CRISPR–cas loci into distinct classes, types and subtypes is presented.
IntaRNA: efficient prediction of bacterial sRNA targets incorporating target site accessibility and seed regions
INTARNA, a new general and fast approach to the prediction of RNA–RNA interactions incorporating accessibility of target sites as well as the existence of a user-definable seed, is introduced.
IntaRNA 2.0: enhanced and customizable prediction of RNA–RNA interactions
IntaRNAv2 is introduced, which enables enhanced parameterization as well as fully customizable control over the prediction modes and output formats and has been included into the Galaxy workflow framework and its already established web interface enables ad hoc usage.
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.
GraphProt: modeling binding preferences of RNA-binding proteins
GraphProt models predict that predicted Ago2 targets display higher levels of expression upon Ago2 knockdown, whereas control targets do not, and estimated binding affinities correlate with experimental measurements.
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.
Evolutionary classification of CRISPR–Cas systems: a burst of class 2 and derived variants
An updated evolutionary classification of CRISPR–Cas systems and cas genes is provided, with an emphasis on the major developments that have occurred since the publication of the latest classification, in 2015, which includes 2 classes, 6 types and 33 subtypes.
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.
INFO-RNA - a fast approach to inverse RNA folding
A new algorithm for the inverse folding problem (INFO-RNA) is introduced 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.
CopraRNA and IntaRNA: predicting small RNA targets, networks and interaction domains
The functionality of the CopraRNA and IntaRNA webservers are introduced and detailed explanations on their postprocessing functionalities are given.