Proksee now reports raw (unadjusted) values for base composition plots. These values can be obtained by hovering over plot regions, and summary statistics (minimum, maximum, and average values) can be accessed in the Plots Panel.

The tool documentation has been updated to better describe how the GC Content and GC Skew plot values are generated and displayed.

GC Content values are calculated using a sliding window and the formula (G+C)/(Length), which leads to values between 0 and 1.

GC Skew values are calculated using a sliding window and the formula (G-C)/(G+C), which leads to values between -1 and 1.

The Y-axis range of displayed plots is automatically set to the min/max values for the plot (e.g. if the minimum score is 0.26, the Y-axis will start at 0.26).

This Y-axis adjustment allows the full plotting space to be utilized and variation to be more easily observed.

A new tool has been added to Proksee:

• Bakta
  • Annotate the genome sequence with Bakta.
  • Paper: Bakta: rapid and standardized annotation of bacterial genomes via alignment-free sequence identification

A new tool has been added to Proksee:

• MITOS
  • Annotate metazoan mitochondrial genomes with MITOS 2.
  • Paper: Improved annotation of protein-coding genes boundaries in metazoan mitochondrial genomes

A new tool has been added to Proksee:

• Track List Caption (Map Refinements)
  • Creates a list of visible track rings (circular) or lanes (linear)
  • This list can be added to the map as a caption or copied to the clipboard
  • The tool is also accessible from the top of the Track Pane by clicking the button

A new tool has been added to Proksee:

• BLAST Formatter (Map Refinements)
  • Applies a customizable color scheme to the results from one or more BLAST comparisons based on their percent identity.
  • Sorts BLAST tracks based on how similar they are to the map genome.

Here's an example showing E. coli str. K-12 compared against five other E. coli genomes. Before formatting (top), the hits are colored based on BLAST track (i.e. the hits from a particular job are all assigned the same color). After using BLAST Formatter (bottom), the hits are colored based on percent identity.

Within the BLAST Formatter tool you can choose the percent identity cut-offs and color scheme. A graph showing the distribution of the percent identities for the current BLAST results can be used to choose informative cut-offs.

The Proksee color picker has been completely redesigned with several new features:

• Editable RGB and Hex color values.
• Swatch mode for quickly selecting predefined colors.
• Favorites for saving and using colors across maps.

More details and tips for using the color picker can be found in help.

CARD RGI has been updated to 6.0.2 (from 5.2.1).

This version of CARD removed the option --exclude_nudge and replaced it with --include_nudge for RGI main so nudged results are no longer included in default RGI main output.

New Format Bar Buttons:

Toggle Legend
Toggle Default Labels
Toggle Angled Labels

Label Notes

• Default labels work best for maps with many evenly distributed labels.
• Angled labels work best for maps with fewer labels or with labels that are clustered together.
• Both default and angled labels can be turned off to show no labels.

New Map Keyboard Shortcuts

• [↓]: Zoom In
• [↑]: Zoom Out
• [←]: Move Left/Counter-Clockwise
• [→]: Move Right/Clockwise
• [ . ]: Reset Map
• [ / ]: Toggle map format between linear and circular

If you use Proksee in your research, please cite our new paper:

Grant JR, Enns E, Marinier E, Mandal A, Herman EK, Chen C, Graham M, Van Domselaar G, and Stothard P
Proksee: in-depth characterization and visualization of bacterial genomes
Nucleic Acids Ressearch, 2023, gkad326, https://doi.org/10.1093/nar/gkad326

Download PDF

Two new tools have been added to Proksee:

• VirSorter
  • Detect dsDNA and ssDNA virus genomes (phage).
  • Paper: VirSorter2: a multi-classifier, expert-guided approach to detect diverse DNA and RNA viruses
• FastANI
  • Fast alignment-free computation of whole-genome Average Nucleotide Identity (ANI).
  • Paper: High throughput ANI analysis of 90K prokaryotic genomes reveals clear species boundaries

A new tool has been added to Proksee:

• mobileOG-db
  • Find mobile genetic elements (MGEs) in your sequence grouped into 5 major categories: integration/excision, replication/recombination/repair, transfer, stability/transfer/defense, and phage-specific processes.
  • Paper: mobileOG-db: a Manually Curated Database of Protein Families Mediating the Life Cycle of Bacterial Mobile Genetic Elements

Proksee can now assembly your raw sequence reads into an assembled genome. Proksee Assemble is undergoing beta testing. To try it out click on the Reads tab on the New Project page.

If you have any problems or suggestions, let us know at Assembly Feedback.

A new tool has been added to Proksee:

• Alien Hunter
  • Predicts putative Horizontal Gene Transfer (HGT) events with the implementation of Interpolated Variable Order Motifs (IVOMs)
  • Paper: Interpolated variable order motifs for identification of horizontally acquired DNA: revisiting the Salmonella pathogenicity islands

Two new tools have been added to Proksee:

• CRISPR/Cas Finder
  • Search for CRISPR Arrays and their associated (Cas) proteins.
  • Paper: CRISPRCasFinder, an update of CRISRFinder, includes a portable version, enhanced performance and integrates search for Cas proteins
• pLannotate
  • Annotate engineered plasmids. Sequences must be less 50,000 bp.
  • Paper: pLannotate: engineered plasmid annotation

A new Help page has been added and can be accessed from the Navigation bar.

In addition, help icons can be found throughout Proksee. Hovering over the icon will display a popup showing information pulled from the help page. Clicking on the help icon will open a new tab and take you directly to appropriate help section.

Maps can now be downloaded as SVG images:

Proksee was presented as a poster at the BioNet 2022 Conference.