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List of Software#

CEA
CKSAAP-Palm
CNetA
CNetQ
Corbi
DGPsubNet
DeterminePPI
EllipsoidFN
GNTInfer
GRNInfer
HMC
InferPPI
LOHCRP
MCDGPA
MDCInfer
MILP_k
MNAligner
MarkRank
Mimic
NCCAUC
NRWRH
NetGen
NetPredATC
PECA
PRNA
PSN
PTG
PTMPred
PreDR
PrePPItar
QMC
SABIC
SANA
Samo
VPECA

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 (3)#

  • 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 15-May-2011 16:00 by LingyunWu.