hhu Institut für Physikalische Biologie ipb

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Multiple alignments of non-coding RNAs.
Prediction of melting transitions of dsRNA, DNA or RNA/DNA hybrids.
Tinoco Plot
Display possible secondary structure elements in single stranded RNA or DNA.
Dot Plot
Display possible intermolecular secondary structure elements between two single stranded RNA or DNA molecules..
Langmuir Plot
Evaluate binding curves (adsorption isotherms) according to Hill or Langmuir.
Static pages
International Conference on Viroids and Viroid-Like RNAs (2015)
novoMIR (original software; 2010)
Tool for de novo prediction of microRNA-coding regions in a single plant genome as described by Teune & Steger (2010) J. Nucleic Acids 2010.
  • novoMIR update (2011)
  • Short description of novoMIR's output
  • novoMIR update (2014); modifications:
    • the program is able to use the recent version 3.1.4 of RNAshapes (via option -R);
    • the program produces a shortened output which should be much easier to parse than the previous output (still available via option -l):
      • sequence fragments and corresponding pre-miRNA prediction(s) are separated by lines consisting of only `#';
      • last but one and last line of a prediction are the sequence fragment and its structure;
      • each prediction is on a single line;
      • values of a prediction are separated by `&' (id, value, mean value, FWD, FWD structure, REV structure, REV, miRNA(s))
      • a miRNA prediction is either not available (`NA') or a list of position pairs separated by `;'; each pair, separated by `,', are the start and end positions with and without gaps in the FWD/REV sequence
Benchmark RNA alignment database for sequence alignment programs.
ConStruct v3
RNA alignment editor and consensus structure prediction tool.
to Diermann et al. (2010) Characterization of plant miRNAs and small RNAs derived from potato spindle tuber viroid (PSTVd) in infected tomato. Biol. Chem. 391, 1379-1390.
International Conference on Viroids and Viroid-Like RNAs (2008)
to Matousek et al. (2007) Experimental transmission of pospiviroid populations to weed species characteristic of potato and hop fields. J. Virol. 8, 11891-11899.

G. Steger
Last modified: Feb 20 2014