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6 papers found.
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Comparison of efficiency and specificity of CRISPR-associated (Cas) nucleases in plants: An expanded toolkit for precision genome engineering

curation: Nicola J. Patron. Formal analysis: Oleg Raitskin, Christian Schudoma, Nicola J. Patron. Funding acquisition: Nicola J. Patron. Investigation: Oleg Raitskin, Christian Schudoma, Anthony West ... , Nicola J. Patron. Methodology: Oleg Raitskin, Christian Schudoma, Anthony West, Nicola J. Patron. Project administration: Nicola J. Patron. 13 / 17 Resources: Oleg Raitskin, Christian Schudoma, Nicola J

blastjs: a BLAST+ wrapper for Node.js

Background To cope with the ever-increasing amount of sequence data generated in the field of genomics, the demand for efficient and fast database searches that drive functional and structural annotation in both large- and small-scale genome projects is on the rise. The tools of the BLAST+ suite are the most widely employed bioinformatic method for these database searches. Recent...

Lost in folding space? Comparing four variants of the thermodynamic model for RNA secondary structure prediction

Background Many bioinformatics tools for RNA secondary structure analysis are based on a thermodynamic model of RNA folding. They predict a single, "optimal" structure by free energy minimization, they enumerate near-optimal structures, they compute base pair probabilities and dot plots, representative structures of different abstract shapes, or Boltzmann probabilities of...

Modeling RNA loops using sequence homology and geometric constraints

Christian Schudoma 0 Patrick May 0 Dirk Walther 0 Associate Editor: Ivo Hofacker 0 Bioinformatics Group, Max Planck Institute of Molecular Plant Physiology , Am Mhlenberg 1, D-14476 Potsdam-Golm

Sequence–structure relationships in RNA loops: establishing the basis for loop homology modeling

The specific function of RNA molecules frequently resides in their seemingly unstructured loop regions. We performed a systematic analysis of RNA loops extracted from experimentally determined three-dimensional structures of RNA molecules. A comprehensive loop-structure data set was created and organized into distinct clusters based on structural and sequence similarity. We...

Detection and characterization of 3D-signature phosphorylation site motifs and their contribution towards improved phosphorylation site prediction in proteins

, Christian Schudoma1, Wolfram Weckwerth3, Joachim Selbig1,2 and Dirk Walther1 E-mail: Pawel Durek - Christian Schudoma - Wolfram Weckwerth - Joachim Selbig - Dirk Walther - Corresponding author 0