In this work we analyze genomic neighborhood of a gene as a source of functional information. Using concept of Similarity-Neighborhood graph we show presence of non-trivial relations between genomic neighbors in the context of several genomes. We also show that while for prokaryotes the existence of such relations can be deduced from the operonic organization of prokaryotic genomes, these relations can also be detected in the eukaryotic genomes where such organization is not common (with notable exception of Caenorhabditis elegans and possibly othermembers of Nematodae). We demonstrate applicability of the our method for uncovering gene's function and studying properties of genomes. We also demonstrate the techniques and tools developed for the analysis of genomic data. PEDANT genome system has been developed by our group and served as a main foundation for development of Similarity-Neighborhood approach, with the latter coming into life as a separate gene-function prediction tool - SNAPper web server. We discuss the techniques hiding behind our all-against-all protein alignment database, which has been developed as part of PEDANT genome analysis system. Such database is the requirement for nearly any cross-genome comparison approach, as it provides the basis for delineating of orthologous and paralogous groups of genes. One of such approaches - phylogenetic profiling, has been implemented by us in collaboration with Philip Wong and Walid Houry of University of Toronto, as highly flexible Web-based tool called PWP. The Jaba visualisation tool which we developed for manual analysis of the genomes and multiple gene predictions and which has been extensively used in several genome projects, including large eukaryotic genome projects such as Arabidopsis thaliana and Neurospora crassa is also presented.     «

In this work we analyze genomic neighborhood of a gene as a source of functional information. Using concept of Similarity-Neighborhood graph we show presence of non-trivial relations between genomic neighbors in the context of several genomes. We also show that while for prokaryotes the existence of such relations can be deduced from the operonic organization of prokaryotic genomes, these relations can also be detected in the eukaryotic genomes where such organization is not common (with notable...     »

Wir untersuchen genomische Nachbarschaft as eine Quelle funktioneller Informationen über Gene. Basierend auf dem Konzept von Simlarity-Neighborhood Graphen wird gezeigt, wie nicht-triviale Verhältnisse zwischen benachbarten Genen aufgedeckt werden können. Während in Prokaryoten das Vorhandensein solcher Korrelationen auf die Operonstrukturen zurückverfolgt werden kann, wurde dieses Phänomen auch in einigen eukaryontischen Genomen entdeckt, wo Operone in der Regel nicht vorkommen. Wir demonstrieren die Anwendbarkeit dieser Methode zur Genfunktionsvorhersage und Untersuchung von Genomeigenschaften. Darüber hinaus werden folgende Techniken zur Genomanalyse vorgestellt: a) Eine Web-Ressource zur Untersuchung von Similarity-Neighborhood Graphen, b) Die Datenbank von Alignments zur Berechnung von paralogen und orthologen Gengruppen, c) Ein phylogenetic profiling Werkzeug, d) Ein Programm zur Visualisierung genomischer Informationen und multiplen Genvorhersagen.     «

Wir untersuchen genomische Nachbarschaft as eine Quelle funktioneller Informationen über Gene. Basierend auf dem Konzept von Simlarity-Neighborhood Graphen wird gezeigt, wie nicht-triviale Verhältnisse zwischen benachbarten Genen aufgedeckt werden können. Während in Prokaryoten das Vorhandensein solcher Korrelationen auf die Operonstrukturen zurückverfolgt werden kann, wurde dieses Phänomen auch in einigen eukaryontischen Genomen entdeckt, wo Operone in der Regel nicht vorkommen. Wir demonstrier...     »