Viral Genome Compression

  • Lucian Ilie
  • Liviu Tinta
  • Cristian Popescu
  • Kathleen A. Hill
Conference paper
Part of the Lecture Notes in Computer Science book series (LNCS, volume 4287)


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.


viruses viral genomes genome compression overlapping genes shortest common superstring problem exact algorithms approximate solutions lower bounds 


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Copyright information

© Springer-Verlag Berlin Heidelberg 2006

Authors and Affiliations

  • Lucian Ilie
    • 1
  • Liviu Tinta
    • 1
  • Cristian Popescu
    • 1
  • Kathleen A. Hill
    • 2
  1. 1.Department of Computer ScienceUniversity of Western OntarioLondon, OntarioCanada
  2. 2.Department of BiologyUniversity of Western OntarioLondon, OntarioCanada

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