Genome Analysis#

• 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

Molecular Networks#

Gene Regulatory Networks Inference#

• 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#

• 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#

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

Network Alignment#

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

Structure Biology#

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