Searching a pattern in compressed DNA sequences
by Ashutosh Gupta, Suneeta Agarwal
International Journal of Bioinformatics Research and Applications (IJBRA), Vol. 7, No. 2, 2011

Abstract: This paper introduces a novel algorithm for DNA sequence compression that makes use of a transformation and statistical properties within the transformed sequence. A word based tagged code is used for identification of end of code. The word based encoder uses frequency distribution for assigning the code of words. The designed compression algorithm is efficient and effective for DNA sequence compression. As a statistical compression method, it is able to search the pattern inside the compressed text which is useful in knowledge discovery. Experiments show that our algorithm is shown to outperform existing compressors on typical DNA sequence datasets.

Online publication date: Sat, 24-Jan-2015

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