Proksee now includes Snapshots, a convenient way to save and revisit genome map states and share them with others. The new Snapshot button above the map saves the current map state as a Map JSON file on the Proksee server.

A snapshot is functionally equivalent to downloading and reloading the Map (CGView) JSON from the Download Panel, with the added benefit of staying within the project. Snapshots do not include job results, and jobs within the project remain unaffected when viewing or restoring snapshots.

The Download tab has been replaced with a Data tab, which includes both the Download and Snapshots panels. From here, you can restore previous snapshots or enable sharing. Shared snapshots generate a link that can be provided to others. When a shared link is used, it creates a new project based on the snapshot, just as if it were created from a Map JSON file.

A Map Style is a collection of visual settings (e.g. legend colors, label fonts, etc) that can be saved from one map and applied to others via a JSON file. This is ideal for reusing customized styles across multiple maps, saving time and ensuring consistency.

The Map Style button is located in the Display Pane, to the right of the Settings tab button.

The Map Style dialog provides two main functionalities, organized into separate tabs:

• Export: Save your current map settings to a JSON file. A list of customizable settings will be displayed, allowing you to choose which ones to include in the export.
• Import: Apply saved settings from a JSON file to a new map. When importing, you can select specific settings from the list to customize the map as desired.

The feature detail view now includes a new Sequence section at the bottom. You can easily copy the DNA sequence for any feature. If the feature is a CDS, the amino acid sequence is also available for copying. Unless otherwise specified, the amino acid sequence is translated directly from the DNA sequence using the appropriate genetic code.

If the original GenBank or EMBL file contains a qualifier translation for the feature, and it differs from the translation derived from the DNA sequence, the original translation is retained and provided.

This is available for all features in the Features Panel:

The download sequences panel will also use the original translation if available and if the default genetic code is used.

The CGViewBuilder 2.0 parser for converting GenBank, EMBL, and FASTA files into CGView Map JSON has been completely redesigned in JavaScript, bringing several key improvements:

• Enhanced Error Handling: Now supports non-standard GenBank files generated by third-party tools (e.g., SnapGene, Geneious), minimizing parsing errors.
• Improved Performance: Genome files are processed directly in the browser, providing a faster and more streamlined workflow.
• Support for Complex Features: Features with multiple locations are no longer skipped and are displayed as joined feature segments:

• Detailed Log: After uploading a genome, a log is generated that outlines the parsing process and highlights any errors or warnings encountered during the conversion.
• New Import Settings: Access additional options via the settings button:
  • Customizable Feature Names: Select which feature qualifiers to use (and their order) when choosing feature names.
  • Feature Types Selection: Control which feature types to include or exclude from the map.
  • Qualifier Selection: Choose which feature qualifiers to include or exclude. Qualifiers will appear in popups when hovering over features and, in the future, will be viewable, editable, and searchable in the Feature Pane.

The feature tool has been fully rewritten to support a wider range of file types. In addition to CSV/TSV, it now imports features from GFF3, GTF, and BED files. The file format is automatically detected, but if the wrong format is selected, you can manually override it in Import Settings using the settings button. This is also helpful if you have a GTF, GFF3, or BED file but want to import specific columns—simply select TSV, reparse, and choose the desired columns. In the example below, only the type, start and stop positions will be imported from the provided GTF file.

A new detailed log is also available. After uploading a features file, a log is generated that outlines the parsing process and highlights any errors or warnings encountered during the conversion.

Two new options have been added to the Separate Features By setting for tracks. In addition to separating features by strand or reading frame, you can now separate them by type or legend. This update displays a new ring or lane on the map for each type or legend, with the rings/lane layers sorted so that those with the most features appear at the bottom or closer to the center of the map.

An optional center line has been added to the map view, providing a useful guide for aligning features, plots, and the sequence. The center line can be easily toggled on or off using the new button in the Format Bar. Customization options, such as color and thickness, are available in the Sidebar for further adjustments.

Default

Customized

Tool options in the Start/Add dialogs now remember changes when rerunning tools. For example, in the BLAST tool, the default value for "Filter low complexity sequences" is Yes. If you change this to No, the tool will remember that change for the next time you run BLAST. These changes are saved in your browser's LocalStorage (similar to cookies).

At the bottom of tool Start/Add dialogs, is a new "Reset Options" button. This button resets the options to the default values. If the options are already set to the defaults the button will be disabled.

CARD RGI has been updated to 6.0.3 (from 6.0.2).

This version of CARD adds HSP subject coordinates and antibiotics to output.

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

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.