Next-generation microbiology: from comparative genomics to gene function

Journal article

Prokaryotic organisms usually possess compact genomes, which are particularly suitable to complete sequencing with existing technologies, which led to an escalating accumulation of available genome data. In response to this ever-expanding repository of information, we introduce ProSt, a computational system designed for the batch computation, storage, and interactive visualization of the values of attributes of prokaryotic genomes. The system allows for parallel attribute value batch computation, dynamically designed to incrementally integrate new attribute values as additional genomes become available. ProSt is flexible permitting the definition of attributes by implementing attribute value computation plugins, supporting several languages (Python, Nim, Rust and Bash). This allows the system to continually evolve in accordance with changing research needs and developments. Additionally, our computation and storage systems maintain comprehensive metadata, thereby enabling data provenance tracking for the computed attribute values

Authors: Kobras, CM; Fenton, AK; Sheppard, SK

• Publication status: Published
• Peer review status: Peer reviewed
• Publisher: BioMed Central
• Journal: Genome Biology
• Volume: 22
• Issue: 1
• Pages: 123-123
• Article number: 123
• Publication date: 2021-04-29
• DOI: 10.1186/s13059-021-02344-9
• EISSN: 1474-760X
• ISSN: 1474-7596
• Language: English
• Keywords: Computational biology; Genome; Biology; Genetics; Function (biology); Gene; Genomics; Human genetics; Comparative genomics