PneumoWiki: A pan-genome-based database for the pathogen Streptococcus pneumoniae

ABSTRACT The Gram-positive bacterium Streptococcus pneumoniae is a major human pathogen that exhibits more than 100 different capsular serotypes and considerable genomic variation. S. pneumoniae is also an important model organism for basic and biomedical research, with a number of strains with different characteristics being used. To address this, we have created the manually curated pan-genome database Pneumo Wiki ( https://pneumowiki.med.uni-greifswald.de ) that integrates genomic data from 43 S. pneumoniae strains with various aspects of functional annotation. All data relating to a specific gene and gene product are compiled on a Gene pag e. In addition to the gene and protein sequences and annotation from NCBI RefSeq, the Gene pages contain data on, for example, gene essentiality, protein function and localization, and transcriptional regulation. The information is supplemented with links to the data sources as well as to other databases and relevant literature. The basic concept of Pneumo Wiki is the interlinked presentation of pan-genome-based and strain-specific information. Therefore, register tabs with strain names at the top of the Gene pages allow switching between orthologous genes and the corresponding pan-genome page. The pan-genome gene pages contain a summary with functional information and the occurrence of the gene, an orthologue table for the 43 S. pneumoniae strains, a multiple-strain genome viewer as well as a protein sequence alignment. Pneumo Wiki was developed as a user-friendly tool and is available free of charge. The data collected in Pneumo Wiki are accessible via various download options to support bioinformatic applications. Overall, Pneumo Wiki is a resource for the pneumococcal research community that supports the analysis and interpretation of research data and, in particular, enables the integration of the knowledge available for different S. pneumoniae strains.