Viral genome compression

Authors:
Lucian Ilie;Liviu Tinta;Cristian Popescu;Kathleen A. Hill
Affiliations:
Department of Computer Science, University of Western Ontario, London, Ontario, Canada;Department of Computer Science, University of Western Ontario, London, Ontario, Canada;Department of Computer Science, University of Western Ontario, London, Ontario, Canada;Department of Biology, University of Western Ontario, London, Ontario, Canada
Venue:
DNA'06 Proceedings of the 12th international conference on DNA Computing
Year:
2006

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Abstract

Viruses compress their genome to reduce space. One of the main techniques is overlapping genes. We model this process by the shortest common superstring problem, that is, we look for the shortest genome which still contains all genes. We give an algorithm for computing optimal solutions which is slow in the number of strings but fast (linear) in their total length. This algorithm is used for a number of viruses with relatively few genes. When the number of genes is larger, we compute approximate solutions using the greedy algorithm which gives an upper bound for the optimal solution. We give also a lower bound for the shortest common superstring problem. The results obtained are then compared with what happens in nature. Remarkably, the compression obtained by viruses is quite high and also very close to the one achieved by modern computers.