List of Software#

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

• 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

Systems Biology#

• MCDGPA: Modularized Candidate Disease Genes Prioritization Algorithm