The various many tools that have been developed or are in development by our lab and their current status (as of Term 4).
Tool | Description | URL | Status |
ViVA (home) | Viral Variome Analyser (ViVA) employs a systematic bioinformatics approach as an ecosystem to understand viral diversity and identify targets that can facilitate diagnostic, surveillance, drug, and vaccine design by processing the large amounts of viral sequence data and metadata produced by genomics, proteomics, and host-pathogen interaction studies, available in public databases, which are continuing to grow rapidly. | Pre-alpha to Alpha [Alignment-dependent] | |
DiMA | Diversity Motif Analyser (DiMA) is a tool designed to facilitate the dissection of protein sequence diversity dynamics for viruses. | Beta [Alignment-dependent] | |
SEVANT (previously VADA) | Sequence divErsity dynamics Visualisers And iNterpreTer (SEVANT) is an all-in-one visualizer-interpreter that uses an embedded Diversity Motif Analyser (DiMA) Python package to quantify and dissect viral protein sequence diversity dynamics. | Alpha [Alignment-dependent] | |
MoSwA | Motif Switch Analyser (MoSwA) is a tool that not only identifies all alignment k-mer positions that exhibit motif switching but also provides a multi-faceted and extensive characterization of the switches. | Beta [Alignment-dependent] | |
CROSTA (previously ATAT) | Cross-Species Transmissibility Analyser (CROSTA) compares the viral protein sequence of two host populations (donor and recipient) that are co-aligned and are analyzed for zoonotic transmission. | Alpha [Alignment-dependent] | |
IDTA | Inhibitory Drug Target Analyser (IDTA) is part of the ViVA ecosystem to evaluate the potential of conserved sites for use as pockets for drug design. | Pre-alpha [Alignment-dependent] | |
ViTA | Vaccine Target Analyser (VITA) is part of the ViVA ecosystem that aims to give the users the viral sequences that could be used as effective vaccine targets. | Alpha [Alignment-dependent] | |
DiTA | Diagnostics Target Analyser (DiTA) is part of the ViVA ecosystem that aims to evaluate the diagnostic potential of highly conserved sequences. | Pre-alpha [Alignment-dependent] | |
VIM | Viva Integration Module (VIM) is the web-based graphical user interface (GUI) for all the analytical modules of VIVA. | Alpha | |
ShareomeMapper | A tool to delineate the host-pathogen shareome across taxonomic lineages | Hyperlink 1(private access) | Gamma [Alignment-independent/free] |
UNIQmın | An alignment-independent tool for the study of pathogen sequence diversity | Released/Published [Alignment-independent/free] | |
VIROMEdash | A visualizer for NCBI Virus that mines the existing records and presents insights over five major metadata dimensions (taxonomy class, host-organism, geography, collection date, and Baltimore class). | Released/Published [Alignment-independent/free] | |
repmsa | Creating a percentage identity matrix from a multiple sequence alignment and then ranking them to select the best sequence representetive in the Multiple Sequence Alignment. repmsa ranks the sequences based on highest identity. | Released/Published [Alignment-independent/free] |