Reference Sequence Construction for Relative Compression of Genomes

Details Reference Sequence Construction for Relative Compression of Genomes Reference Sequence Construction for Relative Compression of Genomes

2011-06-20

arxiv.org/abs/1106.3791v1

Biology

Quantitative Biology

Quantitative Methods

12 pages, 2 figures, to appear in the Proceedings of SPIRE2011 as a short paper

Scientific paper

Relative compression, where a set of similar strings are compressed with respect to a reference string, is a very effective method of compressing DNA datasets containing multiple similar sequences. Relative compression is fast to perform and also supports rapid random access to the underlying data. The main difficulty of relative compression is in selecting an appropriate reference sequence. In this paper, we explore using the dictionary of repeats generated by Comrad, Re-pair and Dna-x algorithms as reference sequences for relative compression. We show this technique allows better compression and supports random access just as well. The technique also allows more general repetitive datasets to be compressed using relative compression.

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