Basel, 2001/02/21
Genedata, the leading provider of enterprise-based bioinformatics solutions, today announced the release of version 3.5 of its Phylosopher system.
Phylosopher is a highly innovative computational system for the prediction of gene function based on exhaustive comparison of complete genomes. The comparison of completely sequenced genomes is key to a deeper understanding of the genetic interrelationships of bacteria, fungi, plants, animals and humans. Phylosopher is already widely used for pharmaceutical and agrobiological applications, particularly for developing novel antibacterial and antifungal agents, as well as identifying diagnostic markers and optimizing metabolic engineering processes.
From a technological standpoint, Phylosopher is not only a data analysis system, but also provides a fully integrated relational database system that can be used as a company-wide research management platform for helping scientists answer challenging questions arising from the deciphered book of life.
Phylosopher is the only system on the market able to analyze hundreds of complete genomes in parallel. This scalability is due to a sophisticated large-scale genome comparison technology and a high-throughput functional analysis suite specifically developed for characterizing the basic functions of life on a genetic basis. Phylosopher version 3.5 comes with all publicly available genomes, which are currently 47 microbial and higher eukaryotic genomes. A major component of Phylosopher 3.5 is the proprietary functional annotation database, which represents a comprehensive functional encyclopaedia of these genomes. Built-in project management capabilities facilitate the integration of the customer's in-house data and supplement the genomic information with experimentally-derived data, as chemical data, high-throughput screening data or proprietary phenotype data.
With every additional genome integrated in Phylosopher, the immense diversity of nature becomes more apparent. Evolution seems to have been much more complex than the few commonly used model organisms and many textbooks suggested. Nature's diversity generated a potential that is just about to open up to scientists. The analysis tools in the new version provide the means for numerous novel applications, including automated in-genome screening for commercially relevant natural products, the identification of bioactive molecules produced by microbes, the elucidation of novel species-specific diagnostic markers, and the spotting of bottlenecks in industrial fermentation processes. The new version of Phylosopher also features tools to understand biochemical reactions, pathways, and regulatory networks that are involved in commercially important environmental processes, such as the bioremediation of metals and radionuclides, cellulose degradation and the microbial production, conversion, and conservation of energy in fuels, chemicals, and chemical feedstock.
A major break-through is Phylosopher's innovative Expression Browser, complementing Genedata's Expressionist system. It allows the analysis of gene expression data from microarray technologies in its genomic context. It is the only system available that permits a crossspecies gene expression analysis by comparing subtle differences in the regulatory modes of similar biosynthetic pathways in different individuals, strains and species. Unique sequence analysis tools pinpoint the regulatory genetic elements on the genomic DNA, which can be correlated with the transcription control of induced or repressed gene activity. Analyzing the enormous variety of regulatory networks in different species and their interaction with developmental and metabolic pathways will unravel the complete anatomy of the genomic world.