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Background

Everything started with analysis of Flaviviruses. These single-stranded, positive-sense RNA viruses are very important pathogens as they can infect humans as well as living stock and cause severe diseases. Human related diseases include West-Nile fever, Dengue, Zika, yellow fever and tick-borne encephalitis. The genome consists of one open reading frame (ORF) with a 5'- as well as 3'-untranslated region (UTR). The viruses are usually transmitted by arthropod hosts, therefore they need to be adopted to two very different hosts and their respective immune responses. Interestingly, the UTRs are responsible for regulation of proliferation and reproduction in these hosts. In these UTRs the RNA forms secondary structures and these structures mediate the regulatory functions. To investigate these functions, covariance models (CMs) are used. These models contain sequence AND structure information rather than sequence information solely. To grasp all the information provided by using these CM the visualisation tool CMviz was born.

What is CMviz?

CMviz is an online tool for visualising covariance models in nucleotide sequences. These covariance models are built using the Infernal toolkit and can be used to perform searches in large sequence databases. The output files generated by Infernal are plain text files with a size of several megabytes. Extracting information from such large text files is tedious, but visualisation can help—thus CMviz was created.

Implementation

To reach a broad range of users, CMviz is implemented as a web application. As a framework the Django webframework was used. Django is written in Python3 and is an easy-to-use web framework with a large community. The visualisation is done using D3.