ArticleNucleic acids research2025
BASys2: a next-generation bacterial genome annotation system.
Article in Nucleic acids research, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 2 papers.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
2 citing papers in PubMed.
- MiMeDB 2.0: the Human Microbial Metabolome Database for 2026.Nucleic acids research · 2026Article
- Bioinformatic tools for microbiome analysis: from raw sequences to biological insights.Frontiers in microbiology · 2026Review
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
8 authors.
Funding
Abstract
Originally released in 2005, BASys (Bacterial Annotation System) was one of the first web servers to support online bacterial genome annotation and interactive genomic display. Over the past 20 years, web technologies and annotation algorithms have advanced considerably. To keep current with these advances and changing needs of microbial genomics, we have developed BASys2 (Bacterial Annotation System 2.0). BASys2 represents a significant upgrade to BASys, offering much more rapid (up to 8000× faster) and far more complete (2× as many data fields) genome annotation with significantly improved genome visualization capabilities. More specifically, BASys2 reduces annotation time from 24 h to as little as 10 s through a fast genome-matching and a novel annotation transfer strategy. Accepting either FASTA or FASTQ files, BASys2 is able to generate up to 62 annotation fields per gene/protein, leveraging over 30 bioinformatics tools and 10 different databases. Among the more unique features of BASys2 is its extensive support for whole metabolome annotation and complete structural proteome generation. BASys2's new interactive genome viewer allows rapid, dynamic visualization of complete bacterial genome maps with options to display/hide multiple concentric annotation tracks, show/remove color-coded legends, manipulate the genome map, and select/view individual gene and metabolite annotations. Available as a web server, a desktop viewer application, and a locally installable Docker image, BASys2 allows researchers to achieve unprecedented annotation depth and to easily upload, download, and display these rich genome/metabolome annotations. The BASys2 web server is freely accessible at https://basys2.ca.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.