Whats is VIRIDIC and how to cite
VIRIDIC (Virus Intergenomic Distance Calculator) computes pairwise intergenomic distances/similarities amongst viral genomes. The algorithms used are presented in the paper:
Moraru, C., Varsani, A., and Kropinski, A.M. (2020) VIRIDIC – a novel tool to calculate the intergenomic similarities of prokaryote-infecting viruses. Viruses 12(11). https://doi.org/10.3390/v12111268
Important notes:
1. To run VIRIDIC web, upload a single fasta file with all phage genomes of interest, create a project and press run. Save the project ID that will be displayed when the project is created. You will need it to access the data if the calculations take a long time. If you provide an email address, the project ID will be sent to you.
2. In the input fasta file, the identifier of each fasta record should be unique and it should have no spaces. Spaces can be replaced with '_'.
3. VIRIDIC stand-alone is available now (see download tab). You can use it for jobs with high computational demand and/or for implementing it in your own pipelines. It is very easy to install on your own servers (it is wrapped as a Singularity). You can continue to use the VIRIDIC web-service for small to medium projects (e.g. up to 200 phages per project, no viromes please, they will crash our resources and the analysis will fail).
News
VirClust, a tool for hierarchical clustering of viruses, core protein calculation and protein annotation, is now available at virclust.icbm.de .
Developer - Cristina Moraru, PhD
Senior Scientist, Department of The Biology of Geological Processes
Institute for Chemistry and Biology of the Marine Environment
Carl-von-Ossietzky –Str. 9 -11, D-26111 Oldenburg, Germany
Email: liliana.cristina.moraru( at )uni-oldenburg.de
Developer - Cristina Moraru, PhD
Senior Scientist, Department of The Biology of Geological Processes
Institute for Chemistry and Biology of the Marine Environment
Carl-von-Ossietzky –Str. 9 -11, D-26111 Oldenburg, Germany
Email: liliana.cristina.moraru( at )uni-oldenburg.de
Algorithms used by VIRIDIC and how to cite
VIRIDIC (Virus Intergenomic Distance Calculator) computes pairwise intergenomic distances/similarities amongst viral genomes. The algorithms used are presented in the paper “VIRIDIC – a novel tool to calculate the intergenomic similarities of prokaryote-infecting viruses”, co-authored by Cristina Moraru, Arvind Varsani and Andrew Kropinski. You can access a pre-print of this paper here: 10.1101/2020.07.05.188268
Download VIRIDIC stand-alone
Developer - Cristina Moraru, PhD
Senior Scientist, Department of The Biology of Geological Processes
Institute for Chemistry and Biology of the Marine Environment
Carl-von-Ossietzky –Str. 9 -11, D-26111 Oldenburg, Germany
Email: liliana.cristina.moraru( at )uni-oldenburg.de