Overview

MitoFish is a comprehensive and standardized fish mitochondrial genome database.

MitoFish has four main functions, i.e., taxonomy/species search, sequence similarity search, data batch download, and fish mitogenome annotation. The menu bar on the right side allows users to access these functions, and the former two functions are also directly available from the boxes on the top page.

Accordingly, MitoFish mainly assumes four types of users. The first type contains those who have interest in particular species of fish and searches for its mitogenomic data. Users can easily reach the page of the species of interest via the species search function or the taxonomy table. In each species mitogenome page, a user sees a fish picture and a visual image of the annotated circular mitogenome that help visual recognition, and can download mitogenomic sequence and its annotation data. In addition, for further analysis, taxonomic information and links to the external databases are summarized on the same page. Users can apply the downloaded mitogenomes to their analysis directly, or construct PCR primers by taking advantage of the whole mitogenomic sequence and sequence their own samples of the same species or related species for further molecular phylogenetic analysis.

The second type contains those who have any fish mitochondrial DNA sequence and want to identify it or to infer its evolutionary background. For such users, MitoFish provides sequence similarity search function. When a user inputs nucleotide sequence, MitoFish runs blastn search against the mitogenomic or mitogenomic + partial mitochondrial sequence database and shows which species' sequences are similar to the input sequence. Furthermore, links to each mitogenomic data page are created in the search result pages, so that users can easily download sequence that is similar to the input sequence for further analysis.

The third type contains those who are on comparative mitogenomics. MitoFish provides very precise and standardized annotations that are batch downloadable. Users can convert them into concatenated gene sequence or synteny structure tables, and conduct large-scale analysis of mitogenomic evolution.

Finally, the fourth type contains those who sequenced fish mitogenomic sequence for themselves and want its annotation as easily as possible.

For more details, please refer to our References.