Proksee Tools
Below is the current list of tools available to Proksee projects.
To use a tool, first start a project on the New Project page and then
start your tool of interest from the Tool Panel
in the Sidebar.
| Tool List | ||
|---|---|---|
| Name | Version | Description |
| Features | 2.0.3 | Upload feature data from a text file (e.g. CSV, GFF3, GTF, BED). |
| Plots | 1.0.0 | Upload plot data from a text file. |
| Alien Hunter | 1.2.0 | Predict putative Horizontal Gene Transfer (HGT) events. Limited to 1 contig between 20,000 and 1,000,000 bp. |
| GC Content | 1.0.2 | Add a GC Content plot. |
| CARD Resistance Gene Identifier | 1.2.1 | The Comprehensive Antibiotic Resistance Database (CARD) Resistance Gene Identifier (RGI) |
| PHASTEST | 1.0.0 | Detect and annotate prophage regions. |
| Map Builder | 2.0.5 | Builds the initial CGView JSON file from a GenBank, EMBL, FASTA or raw sequence. |
| Bakta | 1.1.0 | Annotate the genome sequence with Bakta. |
| FastANI | 1.1.0 | Fast alignment-free computation of whole-genome Average Nucleotide Identity (ANI). |
| BLAST Formatter | 1.0.3 | Color existing BLAST features by percent identity and sort BLAST tracks by similarity. |
| MITOS | 1.1.3 | Annotate metazoan mitochondrial genomes with MITOS 2. Limited to genomes up to 50 kbp and 10 contigs. |
| GC Skew | 1.0.2 | Add a GC Skew plot. |
| Prokka | 1.2.0 | Annotate the genome sequence with Prokka. |
| VirSorter | 1.1.1 | Detect dsDNA and ssDNA virus genomes (phage). |
| Track List Caption | 1.2.0 | Create a track figure caption describing all the visible tracks. |
| mobileOG-db | 1.1.3 | Find mobile genetic elements (MGEs). |
| Proksee Assemble | 1.3.0 | Assemble sequencing reads with Proksee Assemble. |
| pLannotate | 1.1.0 | Annotate engineered plasmids with pLannotate. Only works with sequences less than 50,000 bp. |
| CRISPR/Cas Finder | 1.1.0 | Find CRISPR arrays and their associated Cas proteins. |
| BLAST | 1.4.1 | Perform a BLAST comparision with another genome sequence. |
| ORFs | 1.0.1 | Find Open Reading Frames (ORFs) |
| Phigaro | 1.0.1 | Detect and annotate prophage regions. |