| Category | Tool (URL) | Features |
|---|---|---|
| Databases | MIRU-VNTRplus | Highly curated, multi-marker database |
| Strain identification by similarity search or tree based analysis. | ||
| Comparative study with reference strains. | ||
| Provides universal standardized nomenclature for MIRU-VNTR types. | ||
| SITVIT | Contains >40K strains, represents global distribution of spoligotypes | |
| Provides universal standardised nomenclature for spoligotype patterns. | ||
| TB-DB | Central repository for annotated genome sequence data, gene expression data. | |
| Access to analytic and visualization tools | ||
| Facilitates genomic study, will reveal new targets for drugs, vaccine antigens, diagnostics. | ||
| Transmission and Mutation Models |
spolTools: Spoligoforests | Visualizes evolutionary relationships between strains. |
| Takes into account domain knowledge about mutation process eg. Probability of length of deletion follows Zipf distribution. | ||
| spolTools:DESTUS | Detect emerging strains. For a given cluster size and estimated ratio of transmission to mutation rate in dataset, if no. of observed mutations is significantly less than predicted, strain is deemed emerging. | |
| Uses mutation model for spoligotype that reflects mutation mechanism of DR region. | ||
| Helps predict outbreaks, focus control e orts. | ||
| Classification | TB-Insight:Rules | Rule based system for classification of MTBC strains using spoligotype and MIRU24 locus |
| Uses Bayes Net to predict modern/ancestral when MIRU24 locus data not available | ||
| Can visualise distribution of clades identified in dataset using spoligoforests. | ||
| TB-Insight:CBN | Probabilistic model that can use di erent blends of biomarkers for lineage prediction. | |
| Exploits known properties and structure of loci. | ||
| TB-Insight:SPOTCLUST | Mixture model based. | |
| Can be used for prediction of lineage. | ||
| Verifies clusters used in SpolDB3. | ||
| Takes into account domain knowledge about spoligotype mutation process. | ||
| Visualization | TB-Insight:Spoligoforests | Provides view of genetic diversity within MTBC population by lineage. |
| Depicts evolutionary relationships between strains based on both spoligotype and MIRU patterns. | ||
| TB-Insight:Host-pathogen maps | Visual representation of patient characteristics eg. country of birth associated with strains represented by one or more bio-markers - spoligotype, MIRU, RFLP. | |
| Helps make associations between patient characteristics and strain groups. | ||
| Helps identify anomalies, and focus control efforts. | ||
| Interactive view of global distribution of strains. | ||
| View of the effect of various patient risk factors. |