Phylogenomics and DNA visualization

Principal Investigator: Dr Oleg Reva

This project addresses the development of an integrated research environment for data mining in DNA sequences. The tools to be developed will be instrumental for:

• Functional annotation and visualization of complete genome sequences including identification of horizontally transferred gene islands
• Reconstruction of genome evolution in a historical perspective
• Facilitating analysis of metagenomic data to profile and identify the taxonomic content and the specific changes in microbial communities
• Environmental monitoring of hazardous pathogens, sanitary indicative and released biocontrol and biotechnological strains

SeqWord is divided into the following program modules:

• Sequence browser – a mean to visualize the genomic fragments belonging to different functional categories (gene islands, functionally indispensable regions, non-coding loci, etc.)
• Sequence identifier – a tool to identify the origin of orphan environmental sequences
• Gene island classifier – a program for an automated retrieval of the horizontally transferred genetic elements and identification of the possible origin and the time of insertion
• Finder of global repeats – a database of signature global genomic repeats of length from 8 through 25 bp suitable for detecting the species of interest in the environmental probes by microarray hybridization or direct sequencing

Development of the project will conform to the standards, rules and formats of the FunGIMS laboratory information management system. The innovative statistical algorithms the SeqWord project is based were thoroughly tested on practice and published previously:

1. Klockgether J, Wurdemann D, Reva O, Wiehlmann L, Tümmler B. Diversity of the abundant pKLC102/PAGI-2 family of genomic islands in Pseudomonas aeruginosa. J Bacteriol. 2006 Dec 28; [Epub ahead of print] 
2. Klockgether J, Reva O, Tümmler B. Spread of genomic islands between clinical and environmental strains. In Logan N., Lappin-Scott, Oyston P. (Eds) Prokaryotic Diversity: Mechanisms and Significance. Cambridge University Press, Cambridge. 187-200.
3. Reva ON, Tümmler B. Differentiation of regions with atypical oligonucleotide composition in bacterial genomes. BMC Bioinformatics. 2005 Oct 14;6:251.
4. Reva ON, Tummler B. Global features of sequences of bacterial chromosomes, plasmids and phages revealed by analysis of oligonucleotide usage patterns. BMC Bioinformatics. 2004 Jul 7;5:90.