GraphProt - modeling binding preferences of RNA-binding proteins

Synopsis

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.

Publication

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

Downloads

• Newer versions of GraphProt can be found at GitHub and via bioconda.
• version 1.1.4 GraphProt-1.1.4.tar.bz2 (February 2017)
  
  • additionaly generate structure motif in paired/upaired representation
• version 1.1.3 GraphProt-1.1.3.tar.bz2 (September 2016)
  
  • read model parameters from file
  • select number of sequences to use for motif
  • predict profiles for sequence-and-structure models on sequences of arbitrary length
  • bugfixes related to current versions of perl 5
• version 1.1.1 GraphProt-1.1.1.tar.bz2 (June 2014)
  
  • include predicted margins with crossvalidation 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
    

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?

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