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List of Software#

  1. ADR
  2. CKSAAP-Palm
  3. DeterminePPI
  4. GNTInfer
  5. GRNInfer
  6. HMC
  7. InferPPI
  8. LOHCRP
  9. MCDGPA
  10. MDCInfer
  11. MNAligner
  12. ModularityOptimization
  13. NRWRH
  14. PPICPM
  15. PPINA
  16. PRNA
  17. PSN
  18. PTG
  19. PTMPred
  20. SABIC
  21. Samo
  22. SANA
  23. StruComp

Genome Analysis (6)#

  • HMC: Haplotype inference tool based on Markov Chain model
  • PTG: Pasimonious tree-grow method for haplotype inference
  • LOHCRP: LOH inference and segmentation tool based on conditional random field model
  • CKSAAP-Palm: A tool for predicting palmitoylation sites from protein sequences
  • PTMPred: A tool for predicting post-transcriptional modification sites from protein sequences
  • PRNA: Prediction of protein-RNA binding sites by a random forest method with combined features

Molecular Networks (9)#

Gene Regulatory Networks Inference (2)#

  • GNTInfer: Gene network reconstruction tool with compound targets by integrating multiple microarray datasets and prior information
  • GRNInfer: Gene regulatory network inference tool from multiple microarray datasets

PPI Networks Inference (3)#

  • MDCInfer: PPI prediction tool based on multiple domain cooperation analysis
  • DeterminePPI: Inferring protein-protein interactions by parsimony principle
  • InferPPI: Predicting protein interactions based on parsimony tendency of domain interactions

Network Module Analysis (2)#

  • PPICPM: Identification of functional modules in PPI network by clique percolation clustering
  • ModularityOptimization: Modularity optimization in community identification of complex networks

Network Alignment (2)#

  • MNAligner: Alignment of molecular networks by quadratic programming
  • PPINA: Alignment of protein interaction networks by integer quadratic programming

Structure Biology (5)#

  • Samo: Protein structure alignment tool based on multiple objective optimization
  • SANA: Protein Structure Alignment by Neighborhood Alignment
  • SABIC: protein Structure Alignment Based on Internal Coordinates
  • StruComp: Evaluating protein similarity from coarse structures
  • PSN: Protein pocket similarity networks

Systems Biology (2)#

  • ADR: Detecting and analyzing differentially activated pathways in brain regions of Alzheimer's disease patients
  • MCDGPA: Modularized Candidate Disease Genes Prioritization Algorithm
  • NRWRH: Network-based Random Walk with Restart on the Heterogeneous network

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« This particular version was published on 16-Feb-2011 15:20 by LingyunWu.