This note is addressed to biologists and genome curators working on Plasmodium species, as well as to evolutionary biologists interested in comparing Plasmodium genes and/or their domain architectures, and to computational biologists interested in domain architectures and annotation of diverged sequences.
Plasmobase has been developed for you! From its release in June 2017, the server has been accessed 268 times from all over the world.
Plasmobase is a database for the comparative study of Plasmodium genomes. It proposes a visualisation of domain architectures in 11 Plasmodium complete genomes available in PlasmoDB and it allows for an easy comparison among domain architectures within Plasmodium species and in all other species in UniProt.
Plasmobase provides a new domain annotation! Indeed, the architectures reported in Plasmobase were obtained by applying our state-of-the-art methods, DAMA (Bernardes et al. Bioinformatics, Epub 2015) and CLADE (Bernardes et al. PLoS Computational Biology, Epub 2016) to the 11 Plasmodium genomes.
This study of the 11 Plasmodium species demonstrates that domain architectures greatly augment the trust on annotation and can be very useful in evaluating the functional role of a protein. Domain co-occurrence becomes particularly important for genomes (and assembled metagenomes) that are hard to annotate because of sequence divergence. We believe that in the future, genes in genomes will be looked more and more through the eyes of their domain architecture, and Plasmobase provides a novel step in the construction of these analyses platforms.
The annotations integrated in Plasmobase propose a quite large improvement on the 11 Plasmodium species. A friendly interface allows users to interact with the platform to search for new domain annotations, compare them with existing domain co-occurrences, and detect possible annotation errors.
If you have any suggestion or observations on Plasmobase, we will be glad to collaborate with you to improve this server that wants to be useful to the community!