orthoDeprime: A Tool for Heuristic Cograph Editing on Estimated Orthology Graphs Bachelor’s Thesis

It is a common task in modern biology to analyze or reconstruct the relationship of different species. Since it is assumed that related species share a common ancestor species, many genes are shared between those. Two genes from different species are called orthologous, if they originate from the same gene in their common ancestor species. An orthology graph on a set of genes X is the graph with a set of nodes X where any two nodes are connected if and only if they represent orthologous genes. Recently, it has been discovered that a valid orthology graph is a cograph . However, the true orthology relation for X is unknown in practical applications, so it has to be estimated with an orthology detection tool. An example of such a program is POFF which uses sequence similarity and synteny information to determine orthologous genes in a given set of sequences. Unfortunately, errors are introduced by this estimation such that the orthology graph constructed from the output of POFF will in general not be a cograph. This work focuses on the task of modifying estimated orthology graphs by adding and removing edges in a way that it becomes a cograph. This problem is known as cograph editing and is in general NP -complete, which is why a heuristic approach is chosen. The motivation of the cograph editing process lies in the fact that it is possible to reconstruct the evolutionary history of the input genes when the cograph structure is restored. This information can then be used to reconstruct the phylogeny of a set of species. Another benefit is a more accurate orthology prediction resulting from the fact that the edited orthology graph will be more similar to the true one. Selbstständigkeitserklärung: „Ich versichere, dass ich die vorliegende Arbeit selbständig und nur unter Verwendung der angegebenen Quellen und Hilfsmittel angefertigt habe, insbesondere sind wörtliche oder sinngemäße Zitate als solche gekennzeichnet. Mir ist bekannt, dass Zuwiderhandlung auch nachträglich zur Aberkennung des Abschlusses führen kann.“ [Fak14] Leipzig, den Felix Kühnl