Table 1 Current entry points of CAGECAT and their inputs and outputs
Tool | Purpose | Input | Output |
|---|---|---|---|
Cblaster (Search module) | Search homologous gene clusters | FASTA (protein) GenBank NCBI accessions HMM profile identifiers | Interactive hit visualisation (HTML) Summary table Session file (JSON) |
Clinker (Visualisation module) | Visualise genomes containing homologous gene clusters (all vs. all) | GenBank | Interactive cluster visualisation (HTML) |
Recompute | Re-filter a previous search with new parameters | Session file output of cblaster search (JSON format) | Interactive hit visualisation (HTML) Summary table Session file (JSON) |
Extract sequences | Extract sequences which contain a certain query | Protein sequences (FASTA) Protein headers (TXT) | |
Extract clusters | Extract selected clusters | GenBank | |
Gene Neighborhood Estimation (GNE) | Check intergenic gap from results to optimize parameter | Summary file (TXT)—Interactive visualisation (HTML) | |
Plot clusters | Visualise a search session (align queries to clusters) | Interactive visualisation (HTML) |