Proksee News

User Storage Quota Increased to 500 MB

The default storage quota for Proksee user accounts has increased to 500 MB (from 200 MB).

GC Skew / GC Content Plots Update

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.

New Tool: Bakta

A new tool has been added to Proksee:

New Tool: MITOS

A new tool has been added to Proksee:

New Tool: Track List Caption

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
New Tool: BLAST Formatter

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.

New Color Picker

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 updated to version 6.0.2

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 controls and keyboard shortcuts

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
Proksee had been published in the NAR Web Server Issue (2023)

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

New Tools: VirSorter & FastANI

Two new tools have been added to Proksee:

New Tool: mobileOG-db

A new tool has been added to Proksee:

Proksee Assemble [Beta]: Proksee now accepts sequence reads as inputs

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.

New Tool: Alien Hunter

A new tool has been added to Proksee:

New Tools: CRISPR/Cas Finder & pLannotate

Two new tools have been added to Proksee:

Help page added

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.

SVG downloads now available

Maps can now be downloaded as SVG images:

BioNet 2022 conference poster

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