CBIO tools

• Recombination Detection Program (RDP)

RDP applies a number of recombination detection and analysis methods. It runs well under Windows 95/98/NT/XP/VISTA/7/8 and may/may not run properly under Windows 10. RDP also runs well on most windows emulators. For Mac users PlayOnMac is recommended and for Linux users Wine is recommended.

• PINV (web-based protein interaction viewer)

PINV is an open source, native web application that uses the latest generation of web technologies to offer an interactive view of protein-protein interactions which is easily accessible from any modern browser. PINV enables researchers to explore preloaded or their own data using different methods. The visualization can be manipulated to highlight the proteins or interactions of interest. The resulting graphic can be exported into common graphic formats so it is suitable for publication and sharing purposes.

• Local Galaxy servers

CBIO has a Galaxy installation for developing and running bioinformatics workflows and can provide support for creating custom pipelines or packaging new modules into Galaxy. Setup code and customised tools for EST annotation and mapping of expression data onto pathways can be found here.

• eBioKit

The eBioKit is a system running multiple open source web services on an Apple Mac-mini where all databases are stored locally. This reduces the need for a fast internet connection while giving the users an opportunity to incorporate their data sets in widely used web services. As the eBioKit is a work in progress, more services will be available in the future. The following applications are currently installed:

EnsEMBL, BioMart, NCBI Blast, Galaxy, Jalview, wEMBOSS, MRS, RSAT, Yasara, PLINK, Weblogo and MEGAN

Our local instance is hosted here . Please note that the instance is only accessible within the UCT network.

• ProbeSearcher

Find the right chip for your experiment.

• IT-GOM (Integrated Tool for IC-based GO Semantic Similarity Measures)

This tool provides the information content (IC) of GO terms, semantic similarity between GO terms and GO-based protein functional similarity scores. Users can input UniProt accession numbers or GO IDs.

• SDT (Species Demarcation Tool)

The program allows the demarcation of new virus species based on sequence pairwise similarities. It takes as input a FASTA file of aligned or unaligned DNA sequences and aligns every unique pair of sequences, calculates pairwise similarity scores, and uses a rooted neighbour joining phylogenetic tree to cluster closely related sequences based on similarity scores.

Supported Tools