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The Shortest Common Superstring Problem and Viral Genome Compression

The Shortest Common Superstring Problem and Viral Genome Compression 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. 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 very close to the one achieved by modern computers. http://www.deepdyve.com/assets/images/DeepDyve-Logo-lg.png Fundamenta Informaticae IOS Press

The Shortest Common Superstring Problem and Viral Genome Compression

Fundamenta Informaticae , Volume 73 (1) – Jan 1, 2006

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Publisher
IOS Press
Copyright
Copyright © 2006 by IOS Press, Inc
ISSN
0169-2968
eISSN
1875-8681
Publisher site
See Article on Publisher Site

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. 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 very close to the one achieved by modern computers.

Journal

Fundamenta InformaticaeIOS Press

Published: Jan 1, 2006

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