Mouse SNP Miner database structure. The core database consists of a MySQL relational database containing information associated with predicted functional mouse SNPs from a selected set of mouse inbred strains. A web-based Java Applet module allows querying, visualization, and downloading of information from the database. Basic information about SNP sequence, location, functional consequence, and associated transcript are derived from private and public sequencing efforts via the dbSNP mouse polymorphism collection mapped onto the annotated Ensembl genome. Additional SNP information was extracted from the OMIM, Symatlas, and GO databases. GO clustering by GeneMerge is queried directly by the Applet viewer prior to downloading. PolyPhen assessment of missense mutation consequence was based on Nrdb orthologous protein alignments, PDB structure information, and protein functional annotation from Uniprot. PANTHER assessment of missense mutation consequence was based on a set of HMM protein alignments. Bold font and arrows pointing out of the database indicate the existence of direct web links from our database to associated database entries.