About BASys2

BASys2 (Bacterial Annotation System 2.0). BASys2 represents a significant upgrade to our previous web server known as BASys (originally released in 2005). This new version offers much more rapid (up to 8000X faster) and far more complete (2X as many data fields) genome annotation than the original BASys web server. BASys2 also offers significantly improved genome visualization capabilities.

More specifically, BASys2 reduces annotation time from 24 hours for a single bacterial genome to as little as 10 seconds!! This is done through a fast genome-matching algorithm and a novel annotation transfer strategy that was developed specifically for BASys2. BASys2 can now accept either FASTA or FASTQ files. The support for FASTQ files means that BASys2 can now (rapidly) assemble and annotate raw DNA sequence files as they come off a DNA sequencer.

The depth and quality of BASys2 annotation has been significantly improved. BASys2 now identifies all gene types (protein-coding, tRNA, rRNA, etc.) and is able to generate up to 62 annotation fields per gene/protein by leveraging over 30 different bioinformatics tools and 10 different databases. Annotations include deailed structural, functional, and statistical information, with results available for download in JSON and/or GenBank format. Among the more unique features of BASys2 is its extensive support for whole metabolome annotation and complete structural proteome generation (with 3D structures generated via homology modeling and AlphaFold2). BASys2 delivers fast, extensive, and high-quality genome annotations that rival or exceed those in well established, highly curated databases like UniProt

BASys2’s new interactive genome viewer allows rapid, dynamic, multi-resolution visualization of complete bacterial genome maps with options to display/hide multiple concentric annotation tracks, show/remove colour-coded legends, manipulate the genome map and select/view individual gene and metabolite annotations through clickable Genecards and Metabocards. Available as a web server, a desktop viewer application and a Docker image for local installation, BASys2 allows researchers to achieve unprecedented annotation depth and to easily upload, download and display these rich genome/metabolome annotations.