Database Commons

a catalog of worldwide biological databases

The MITOchondrial genome database of metaZOAns (MitoZoa) is a public resource for comparative analyses of metazoan mitochondrial genomes (mtDNA) at both the sequence and genomic organizational levels. The main characteristics of the MitoZoa database are the careful revision of mtDNA entry annotations and the possibility of retrieving gene order and non-coding region (NCR) data in appropriate formats. The MitoZoa retrieval system enables basic and complex queries at various taxonomic levels using different search menus. MitoZoa 2.0 has been enhanced in several aspects, including: a re-annotation pipeline to check the correctness of protein-coding gene predictions; a standardized annotation of introns and of precursor ORFs whose functionality is post-transcriptionally recovered by RNA editing or programmed translational frameshifting; updates of taxon-related fields and a BLAST sequence similarity search tool. Database novelties and the definition of standard mtDNA annotation rules, together with the user-friendly retrieval system and the BLAST service, make MitoZoa a valuable resource for comparative and evolutionary analyses as well as a reference database to assist in the annotation of novel mtDNA sequences. MitoZoa is freely accessible at http://www.caspur.it/mitozoa.

MitoZoa is a relational database collecting curated metazoan entries of complete or nearly complete mitochondrial genomes (mtDNA), specifically designed to assist comparative studies of mitochondrial genome-level features in a given taxon or in congeneric species of Metazoa. The principal novelties of MitoZoa are extensive corrections/improvements of the mtDNA annotations and the possibility of easily searching for data on: (1) gene order, a genomic feature useful as phylogenetic marker; (2) sequence, size and location of non-coding regions, likely containing the regulatory signals for mtDNA replication and transcription; (3) mt features/sequences of congeneric species, where saturation phenomena in nucleotide substitutions and gene order changes are expected to be absent or at least minimal. In addition, MitoZoa allows the exploration of basic mt features such as molecule topology, genetic code, gene content, and compositional parameters of the entire genome. Finally, in order to facilitate downstream analyses of retrieved data, MitoZoa entry lists can be visualized and downloaded in a tabular format, while sequences and gene order data are provided in FASTA and FASTA-like formats, respectively. The MitoZoa database is available at http://www.caspur.it/mitozoa.