Konferenzbeitrag
Syntenic layout of two assemblies of related genomes
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Text/Conference Paper
Datum
2004
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Quelle
German Conference on Bioinformatics 2004, GCB 2004
Regular Research Papers
Verlag
Gesellschaft für Informatik e.V.
Zusammenfassung
To facilitate research in comparative genomics, sequencing projects are increasingly aimed at assembling the genomes of closely related organisms. Given two incomplete assemblies of two related genomes, the question arises how to use the similarity of the two sequences to obtain a better ordering and orientation of both assemblies. In this paper, we formalize this question as the Optimal Syntenic Layout problem, show that it is in general NP-hard, but that it can be solved well in practice using an algorithm based on maximal graph matching. We illustrate the problem using different assemblies of two strains of Bdellovibrio bacteriovorus.