GeneGA

GeneGA is a software tool for RNA secondary structure prediction and analysis. It is part of the ViennaRNA Package, which has been widely used for nearly two decades. The new version, ViennaRNA Package 2.0, incorporates major changes and improvements, including:

1. Updated energy model and parameters for more accurate predictions.

2. Support for multi-core CPUs to enable concurrent computations via OpenMP.

3. Expanded set of tools for assessing RNA-RNA interactions and restricted ensembles of structures.

4. Additional output information includes centroid structures, maximum expected accuracy structures derived from base pairing probabilities, and z-scores for locally stable secondary structures.

Topic

Gene expression;RNA

Detail

  • Operation: Codon usage bias plotting;Codon usage analysis

  • Software interface: Command-line user interface, Library

  • Language: R

  • License: GNU General Public License, version 2

  • Cost: Free

  • Version name: 1.54.0

  • Credit: GEN-AU projects "regulatory non coding RNA" and "Bioinformatics Integration Network III", the Austrian FWF project "SFB F43 RNA regulation of the transcriptome", the European Union FP-7 project QUANTOMICS, and Deutsche Forschungsgemeinschaft.

  • Input: FASTA

  • Output: -

  • Contact: Zhenpeng Li zpli21@gmail.com

  • Collection: -

  • Maturity: Mature

Publications

Download and documentation

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