Special projects between Bavaria and Georgia

Bioinformatics
Technische Universität München

Biomedical Engineering
Georgia Institute of Technology

Knowledge Base on Genes and Proteins of Entire Microbial Ecosystems

Recent advent of shotgun sequencing of DNA molecules isolated from microbial communities made a revolution in exploration of microbial world. We propose a collaborative project to develop a knowledge base for genes residing in metagenomes and proteins encoded in these genes. Genes predicted by the GeneMark software system developed at Georgia Tech will be annotated by a computational pipeline including two tightly integrated tools developed at the Technical University of Munich. The SIMAP database which currently provides the pre-calculated sequence similarity network of 17 million proteins will be extended to include metagenomic proteins. The PEDANT software suite will then be used to conduct exhaustive functional and structural characterization of gene products and make this annotation available via the Internet. The project will result in the largest publicly available resource of functional information for metagenomic sequences.