KRISP can provide computational services to both academic and to industrial partners (within the context of grants contracts or consultancy services). Please contact us for further information. We have access a wide range of standard life science applications (many optimized for the HPC environment) and databases are available. Additional applications or databases can be hosted on request. Arrangements can also be made to secure proprietary data. We have access to four HPCs (see KRISP Toys) and have developed many bioinformatics tools and databases that are openly accessible.
This tool is designed to use phylogenetic methods in order to identify the HIV-1 subtype of a specific sequence. The sequence is analysed for recombination using bootscanning methods. The version 3 contains new CRFs (CRF01_AE to CRF47_BF).
This is the first version of our Arbovirus typing tool for Chikungunya, Dengue, Yellow Fever and Zika
This is the first version of the Yellow Fever typing tool, which uses phylogenetic analysis to identify the species and genotype of the virus.
Phylogenetic tool to identify the HIV-1 subtypes and recombinants. Query sequences are analysed for recombination using bootscanning methods. The version 3 contains new CRFs (CRF01_AE to CRF47_BF).
Phylogenetic tool to identify the Human Herpesvirus 8 (HHV-8) subtypes and recombinants. Query sequences are analysed against the complete K1 reference sequences for HHV8 subtypes A, A5, B, C, D and E.
Phylogenetic tool to identify the Human Papillomavirus (HPV) subtypes and species. Query sequences are analysed against the complete L1 reference sequences for HPV and involve the construction of a phylogenetic tree using HKY distance method with gamma distribution in PAUP* software. The HHV8 subtypes and sub-groups are identified.
A curated public database designed to represent, store, and analyze the divergent forms of data underlying HIV drug resistance
The RNA Virus Database is a database and web application describing the genome organization and providing analytical tools for all known species of RNA virus.
Online web interface that provides an interface to identify phylotypes and allows for exploratory analyses of very large data sets.
Blast using local databases at our servers. It includes HIV Genbank, Subtype Reference Dataset and HXB2 reference sequence databases
Online web version for BlastAlign software application
Tool to determine quality and contamination of sequences using local Blast
Online tools for searching for epitopes using local Blast
The aim of the Genomics Facility is to setup one of the world's most advanced and respected genetic sequencing systems to UKZN in order to enable and support world-class genomics research in Africa. Our objective is to use NextGen sequencing and bioinformatics to answer scientific questions that are of local, national and international importance. Collaborators are welcome to apply for projects to generate HIV, TB, 16S and host genomic data.
Contains information about each HIV-1 gene product in regard to expression, functional activities, and interactions with viral and host macromolecules
Set of PAUP* scripts to contruct maximum likelihood trees
Download phylotype standard alone interfaces for Mac OS X, Linux and Windows system. A batch and command line version for large analysis is also available.
RegaDB provides researchers with a mechanism to collect data in a uniform format and offers them a canvas to make newly developed bioinformatics tools available to clinicians and virologists through a user friendly interface.
Genetic Data Environment (GDE) interface for HIV-1 coded in Linux Operation System