MSProGene

MSProGene is a method for integrative proteogenomic analysis that combines RNA-Seq driven transcript databases with peptide information to predict gene and protein expression levels in unannotated organisms. The software is independent of existing reference databases or annotated SNPs, and avoids the artificial increase of target databases by constructing sample-specific transcripts. MSProGene also creates a network that resolves the ambiguity of shared peptides for protein inference, and is optimized by a maximum-flow algorithm.

Topic

Proteomics;Transcriptomics;RNA-Seq;Molecular interactions, pathways and networks

Detail

  • Operation: Pathway or network prediction

  • Software interface: Command-line user interface

  • Language: Java

  • License: GNU Lesser General Public License, version 3.0

  • Cost: Free

  • Version name: -

  • Credit: Deutsche Forschungsgemeinschaft (DFG).

  • Input: -

  • Output: -

  • Contact: renardb@rki.de

  • Collection: -

  • Maturity: -

Publications

  • MSProGene: integrative proteogenomics beyond six-frames and single nucleotide polymorphisms.
  • Zickmann F and Renard BY. MSProGene: integrative proteogenomics beyond six-frames and single nucleotide polymorphisms. MSProGene: integrative proteogenomics beyond six-frames and single nucleotide polymorphisms. 2015; 31:i106-15. doi: 10.1093/bioinformatics/btv236
  • https://doi.org/10.1093/bioinformatics/btv236
  • PMID: 26072472
  • PMC: PMC4765881

Download and documentation

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