GraphProt

GraphProt - Modeling Binding Preferences of RNA-Binding Proteins

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GraphProt can be used for modeling binding preferences of RNA-binding proteins from high-throughput experiments such as CLIP-seq and RNAcompete. The latest builds and information on the GraphProt bioconda package are available via GitHub.

Downloads

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Software Versions

• Version 1.1.7 (GraphProt-1.1.7.tar.bz2) (September 2017)
  • prepare for distribution via bioconda
  • add pytest testing
  • compile dynamically linked EDeN binary
• Version 1.1.6 (GraphProt-1.1.6.tar.bz2) (September 2017)
  • fix for parameter optimization
• Version 1.1.5 (GraphProt-1.1.5.tar.bz2) (September 2017)
  • add profile calculation for sequence-structure models
• Version 1.1.4 (GraphProt-1.1.4.tar.bz2) (February 2017)
  • Additionally generates structure motifs in paired/unpaired representation.
• Version 1.1.3 (GraphProt-1.1.3.tar.bz2) (September 2016)
  • Reads model parameters from file.
  • Selects the number of sequences to use for motif.
  • Predicts profiles for sequence-and-structure models on sequences of arbitrary length.
  • Bugfixes for current versions of Perl 5.
• Version 1.1.1 (GraphProt-1.1.1.tar.bz2) (June 2014)
  • Includes predicted margins with cross-validation output.
• Version 1.1.0 (GraphProt-1.1.0.tar.bz2) (May 2014)
  • Bugfixes; changed “predict” output to include FASTA ID.
• Version 1.0.1 (GraphProt-1.0.1.tar.bz2) (January 2014)
  • Initial release.

Training and Evaluation Data

• Sequences used to train CLIP-seq models: GraphProt_CLIP_sequences.tar.bz2
• Sequences used to generate CLIP-seq motifs: GraphProt_CLIP_motifseqs.tar.bz2
• Parameters used in GraphProt publication: parameters.tar.bz2
• GraphProt CLIP models: GraphProt_models_CLIP.tar.bz2
• GraphProt RNAcompete models: GraphProt_models_RNAcompete (FTP)
• Sequences used for PTB affinity predictions and Ago2 3’-UTR evaluations: GraphProt_PTB_UTRs.tar.bz2

Problems/Questions?

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For any questions or issues concerning GraphProt, please write an email to:

Publication

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Daniel Maticzka, Sita J. Lange, Fabrizio Costa, and Rolf Backofen GraphProt: modeling binding preferences of RNA-binding proteins Genome Biology, 2014, 15(1), R17.