Collaboration

                                  

This work is supported by the National Bioinformatics Network of South Africa and the African Centre for Gene Technologies.

We collaborate with:

Prof. B. Tuemmler.
Klinishe Forschergruppe OE6711
Medizinische Hochschule Hannover (MHH)
Carl-Neuberg-Strasse 1
D-30625 Hannover , Germany

Description of the research initiative:

One collaborative proposal between Dr. O. Reva and Prof. B. Tuemmler was successfully submitted to the DFG (Deutsche Forschungsgemeinschaft, http://www.dfg.de/en/) and funding was obtained to support work of a PhD student, Colin Davenport, under a shared supervision: "Exploration of oligonucleotide analysis for the data mining of metagenomes" with the following objectives:

 

1. To develop algorithms to collect the vocabulary of overrepresented oligonucleotide "words" in completely sequenced bacterial strains. The words in the dictionaries, favourably heptamers to decamers, should be evenly distributed in the respective genomes and sequence analysis using these words should enable species identification.

2. To test and verify combinations of algorithms of oligonucleotide statistics, favourably for dimers to pentamers a) that optimally exploit the phylogenetic signatures of bacterial sequences to identify major clades in metagenome analysis of microbial communities or b) that have the highest discriminatory potential of the identification of species and genera of interest, particularly pseudomonads.

3. To develop algorithms, web-accessible databases and software that combine approaches 1 and 2 and that either are optimal for differentiating all clades of bacteria (e optimal compmpromise) that are optimal for identification of species and/or genera of interest, particularly pseudomonads.

4. To contribute to the translation of the SeqWord package into JAVA

Prof. D. Frishman

Lehrstuhl fuer Genomorientierte Bioinformatik,
Technische Universitaet Muenchen (TUM)
Am Forum 1, D-85354, Freising, Germany

Description of the research initiative:

The collaboration will aim at sharing expertise on large-scale data analysis and data mining software development (this team has developed an outstanding sequence analysis suite named Pedant-Pro).

Prof. P. Janssen

Laboratory for Radiobiology & Microbiology 
Institute for Radiological Health, Safety & Environmental Sciences                 
Belgian Nuclear Research Centre SCK/CEN        
Boeretang 200, B-2400-MOL, Belgium

Description of the research initiative:

The research team in SCK/CEN currently is involved in a number of projects that could benefit from the use of SeqWord programs, in particular the MISSEX project (concerning the microbial surveying of the International Space Station) but largely also the genome projects on Cupriavidus metallidurans and Arthrospira platensis (i.e. in terms of mobile genetic element (MGE) detection). Likewise the future environmental genomic studies of the group would benefit from this collaboration.

Prof. A. Toussaint and Prof. R. Leplae,
Service de Conformation de Macromolicules Biologiques et de Bioinformatique SCMBB,
University Libre de Bruxelles (ULB)
Campus Plaine - CP 263
Boulevard du Triomphe
1050 Bruxelles , Belgium

Description of the research initiative:

This group has developed the ACLAME database, the major database of mobile genetic elements (MGEs) in the world. The two databases (ACLAME and the database generated in this project) will be linked so as to provide easy access to all information on individual islands and to strengthen the MGE identification facilities.

Prof. Wen-Tso Liu

Division of Environmental Science and Engineering,
National University of Singapore (NUS),
Description of the research initiative
:

Development of a lab-on-a-bead diagnostic technology to monitor pathogenic microorganisms in sea water.