The Gene Neighbourhood Analysis Tool (GNAT) is a generalizable tool used to visualize the genomic neighbourhoods (GNs) of protein(s) of interest and any homologous proteins found within a specified database. Either a protein FASTA file containing the protein(s) of interest or a PSI-BLAST .out file generated by GNAT can be used as input (for more information, see the input help section below). This tool is particularly useful for exploring the genomic neighbourhoods of genes that tend to cluster, such as those in bacterial operons. Thus, the database on the server contains Staphylococcus aureus sequences from NCBI's ftp site.
Upon submitting a sequence to GNAT, the user will be redirected to a page with their job ID, which can be used to access the results when they are ready. GNAT uses the submitted FASTA sequence(s) as PSI-BLAST queries against the Staphylococcus aureus database. The matches found are then used to generate genomic neighbourhoods consisting of the (default=20) genes upstream and downstream of the match proteins. These genomic neighbourhoods are then filtered based on match percent identity (default=30%) and size (default=20%) versus the query protein. The filtered genomic neighbourhoods are then clustered into groups of approximately 20 and visualized using a modified version of clinker to generate interactive plots with the matches labelled. Phylogenetic trees and pie charts are also generated at every step of the pipeline to show the distribution of the matches across the database.
If you found GNAT or AcrVis useful, please cite our preprint posted on bioRxiv:
Timmerman, N. J., Thakurdeen, M., Wilson, R. E. J., Fung, B. C. M., Trost, B., Davidson, A. R., Trost, C. N., & Jin, L. (2025). GNAT: An Interactive Web Tool for Gene Neighbourhood Analysis. bioRxiv 2025.11.03.686425. https://doi.org/10.1101/2025.11.03.686425
GNAT and AcrVis are available to use, free of charge and without sign-up. The original code for both are licensed under MIT Licenses. GNAT and AcrVis use third-party tools with their own licenses. All licensing information can be found in the Licenses section.
The source code for the AcrVis bioinformatic pipeline is available at https://github.com/USask-BINFO/AcrVis.
The source code for the GNAT web application is available at https://github.com/USask-BINFO/gene-neighbourhood-analysis-tool.
All you need to get started on GNAT is the amino acid sequence of a protein of interest (POI). This sequence may be entered into the large text input box displayed on the landing page, which by default has the FASTA Sequence input tab selected. The sequence must be entered in FASTA format, with a header line preceding the sequence line(s); the header line must begin with a greater-than symbol (>). An example of the sequence input is shown in the screenshot below.
PLACEHOLDERNote that GNAT will use the first "word" of the FASTA header line as the label for any detected PSI-BLAST matches to the POI. The first word is defined as the sequence of characters immediately following the greater-than symbol at the start of the header line, and preceding any white-space characters (e.g., space, tab, newline). If a multi-word label is desired, use underscores rather than spaces. In the example above, any matches would be labelled as "AcrIF25".
Depending on the query protein being input, you may wish to change the database being searched. For example, in the screenshot above, we selected the full combined viral and bacterial genomes database, rather than the default viral database. This selection specifies the database to search for homologous proteins, and from which the genomic neighbourhoods are extracted. Thus, select a database in which you expect homologs to be present; for example, using a LacA protein as input, one might select either the E. coli database or the bacterial database, since the lac operon is found in E. coli. The Databases section contains further information on the databases available on GNAT.
Addtl params
Annotations
Upon job submission, you will be redirected to a loading page.
We have provided several sample jobs for users to explore, accessible via the Job Retrieval page.
The interactive features of the GN visualizations may be slow on some browsers. We find Firefox or Google Chrome to be most responsive. If the plots remain unresponsive, it may be due to their size; large visualization file sizes have reduced responsiveness. More genes/GNs in a plot will increase the file size. Further, plots with many similar GNs, and thus more gene-gene links, will be larger, due to the additional link objects.
If you detect a bug, require support, or have a question not answered on this page or our paper, please send an email to gnat@usask.ca with a descriptive subject line.
MIT License
Copyright © 2026 Nolen Timmerman
The following license applies to all original code in this repository. This
repository also incorporates third-party software under separate license
terms; see THIRD_PARTY_LICENSES.txt for details.
Permission is hereby granted, free of charge, to any person obtaining a copy
of this software and associated documentation files (the “Software”), to deal
in the Software without restriction, including without limitation the rights
to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
copies of the Software, and to permit persons to whom the Software is
furnished to do so, subject to the following conditions:
The above copyright notice and this permission notice shall be included in all
copies or substantial portions of the Software.
THE SOFTWARE IS PROVIDED “AS IS”, WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
SOFTWARE.
MIT License
Copyright (c) 2019 Cam Gilchrist
Permission is hereby granted, free of charge, to any person obtaining a copy
of this software and associated documentation files (the "Software"), to deal
in the Software without restriction, including without limitation the rights
to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
copies of the Software, and to permit persons to whom the Software is
furnished to do so, subject to the following conditions:
The above copyright notice and this permission notice shall be included in all
copies or substantial portions of the Software.
THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
SOFTWARE.
PURPOSE
Krona is a flexible tool for exploring the relative proportions of
hierarchical data, such as metagenomic classifications, using a
radial, space-filling display. It is implemented using HTML5 and
JavaScript, allowing charts to be explored locally or served over the
Internet, requiring only a current version of any major web
browser. Krona charts can be created using an Excel template or from
common bioinformatic formats using the provided conversion scripts.
COPYRIGHT LICENSE
Copyright © 2011, Battelle National Biodefense Institute (BNBI);
all rights reserved. Authored by: Brian Ondov, Nicholas Bergman, and
Adam Phillippy
This Software was prepared for the Department of Homeland Security
(DHS) by the Battelle National Biodefense Institute, LLC (BNBI) as
part of contract HSHQDC-07-C-00020 to manage and operate the National
Biodefense Analysis and Countermeasures Center (NBACC), a Federally
Funded Research and Development Center.
Redistribution and use in source and binary forms, with or without
modification, are permitted provided that the following conditions are
met:
* Redistributions of source code must retain the above copyright
notice, this list of conditions and the following disclaimer.
* Redistributions in binary form must reproduce the above copyright
notice, this list of conditions and the following disclaimer in the
documentation and/or other materials provided with the distribution.
* Neither the name of the Battelle National Biodefense Institute nor
the names of its contributors may be used to endorse or promote
products derived from this software without specific prior written
permission.
THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
"AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR
A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT
HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE,
DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY
THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
(INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
TRADEMARK LICENSE
KRONA™ is a trademark of the Department of Homeland Security, and use
of the trademark is subject to the following conditions:
* Distribution of the unchanged, official code/software using the
KRONA™ mark is hereby permitted by the Department of Homeland
Security, provided that the software is distributed without charge
and modification.
* Distribution of altered source code/software using the KRONA™ mark
is not permitted unless written permission has been granted by the
Department of Homeland Security.
PATENTS
The Krona software is not eligible for patent because there have been
previous and open implementations of this visualization method since
the year 2000 (e.g. "Focus+context display and navigation techniques
for enhancing radial, space-filling hierarchy visualizations." Stasko,
J. and Zhang, E. InfoVis, 2000). Krona represents a reimplementation and
application of an existing method to the new domain of
metagenomics. BNBI, as the copyright holders, wish to release Krona
freely and openly as a service to the bioinformatics community.
POINT OF CONTACT
Todd Harrington
General Counsel
Battelle National Biodefense Institute
harringtont@nbacc.net