List of Software#

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