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GNAT: An Interactive Web Tool for Gene Neighbourhood Analysis

Timmerman, N. J.; Thakurdeen, M.; Wilson, R. E. J.; Fung, B.; Trost, B.; Davidson, A. R.; Trost, C. N.; Jin, L.

2025-11-05 bioinformatics
10.1101/2025.11.03.686425 bioRxiv
Show abstract

Given the sequence of a protein, the Gene Neighbourhood Analysis Tool (GNAT) identifies homologues within microbial (bacterial, archaeal, or fungal) or viral databases, aligns and clusters their genomic neighbourhoods (GNs) by similarity, reports the taxonomic distribution of matched genomes, and generates interactive, publication-quality visualizations with customizable annotations, colours, and display options, along with categorical and quantitative summary analytics. GNATs intuitive interface enables a broad community of researchers to generate biological insights from GNs without requiring computational expertise and serves as a comprehensive and versatile platform for easily comparing GNs across the domains of life. GNAT is accessible at https://gnat.usask.ca.

Matching journals

The top 3 journals account for 50% of the predicted probability mass.

1
Nucleic Acids Research
◐ 1281 papers in training set
Top 0.2%
34.6%
Similar papers in this journal
2
NAR Genomics and Bioinformatics
◐ 242 papers in training set
Top 0.1%
15.2%
Similar papers in this journal
3
BMC Bioinformatics
○ 457 papers in training set
Top 0.9%
8.0%
Similar papers in this journal
50% of probability mass above
4
Bioinformatics
◐ 1204 papers in training set
Top 3%
6.8%
Similar papers in this journal
5
Bioinformatics Advances
◐ 203 papers in training set
Top 0.8%
6.3%
Similar papers in this journal
6
mSystems
● 394 papers in training set
Top 2%
3.5%
7
PLOS Computational Biology
● 1863 papers in training set
Top 10%
3.3%
8
Database
◐ 61 papers in training set
Top 0.3%
2.4%
9
Briefings in Bioinformatics
◐ 354 papers in training set
Top 4%
2.1%
10
Genome Biology
○ 637 papers in training set
Top 5%
1.9%
11
GigaScience
◐ 212 papers in training set
Top 3%
1.5%
12
PLOS ONE
● 5266 papers in training set
Top 50%
1.3%
13
BMC Genomics
○ 406 papers in training set
Top 6%
1.1%
14
mSphere
● 302 papers in training set
Top 6%
1.0%
15
Microbial Genomics
● 225 papers in training set
Top 2%
1.0%
16
Computational and Structural Biotechnology Journal
● 242 papers in training set
Top 6%
1.0%
17
Molecular Biology and Evolution
◐ 542 papers in training set
Top 5%
0.9%
18
Proceedings of the National Academy of Sciences
● 2444 papers in training set
Top 44%
0.6%

"Similar papers" are the closest papers from that journal in the model's embedding space. They show what the match is built on, but the ranking comes mostly from a classifier over the whole training set, not from these examples alone.