A new challenge for compression algorithms: Genetic sequences

Grumbach, Stéphane; Tahi, Fariza

doi:10.1016/0306-4573(94)90014-0

Cited by 231 publications

(147 citation statements)

References 10 publications

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“…2), 1,000 human genomes contain less than twice the unique information of one genome. Thus, although individual genomes are not very compressible 12,13 , collections of related genomes are extremely compressible [14][15][16][17] .…”

Section: Sublinear Analysis and Compressed Datamentioning

confidence: 99%

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Compressive genomics

2012

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Section: Sublinear Analysis and Compressed Datamentioning

confidence: 99%

“…As more divergent genomes are added to a database, Many algorithms exist for the compression of genomic data sets purely to reduce the space required for storage and transmission [12][13][14][15]17,18 . Hsi-Yang Fritz et al 18 provide a particularly instructive discussion of the concerns involved.…”

Section: Challenges Of Compressive Algorithmsmentioning

confidence: 99%

Compressive genomics

2012

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“…The compression of DNA sequences is not an easy task. (Grumback and Tahi 1994 [6], Rivals et al 1995 [7]; Chen et al 2000 [8]) DNA sequences consists of only four nucleotides bases {A, C, G, T}. Two bits are enough to store each base.…”

Section: Introductionmentioning

confidence: 99%

A New Revisited Compression Technique through Innovative Partiotion Group Binary Compression: A Novel Approach

Prasad¹

2013

LNSE

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Day by day the ratio of living organisms are increased and its accumation in the bilogical databases creating a major task. In this connectin some of the classical algorithms are strived into the world and fails to compress genetic sequences due to the captcha of alphabets. Existing substitution techniques will work on repetitive and non repetitiveness of bases of DNA and they achieve Best compression rates if any sequence may contain tandem repeats. But the category of grasses like maize and rice contains very less repeats (nearer of 27) over 67789 total bps. By working existing techniques on such sequences the results are not bountiful and running on worst case comparisons. This paper introduces a novel Innovative partition group Binary compression technique yields first art compression rates which is far better than existing techniques. This algorithm is is develpoed based on comparative study of existing algorithms and which is more applicable for non tandem repeats of DNA sequences in genomes

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“…Our interest in compression here is not for saving file space or communication bandwidth, but in measuring the fit between a model and a sequence. Agarawal and States [11] and Grumbach and Tahi [12] recognised the relevance of compression to pattern discovery in biological sequences. Loewenstern and Yianilos [13] modified a popular file compression algorithm for use with DNA sequences by allowing a certain number of mismatches against past 'contexts'.…”

Section: Introductionmentioning

confidence: 99%

Discovering patterns in Plasmodium falciparum genomic DNA

Stern

Allison

Coppel

et al. 2001

Molecular and Biochemical Parasitology

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A method has been developed for discovering patterns in DNA sequences. Loosely based on the well-known Lempel Ziv model for text compression, the model detects repeated sequences in DNA. The repeats can be forward or inverted, and they need not be exact. The method is particularly useful for detecting distantly related sequences, and for finding patterns in sequences of biased nucleotide composition, where spurious patterns are often observed because the bias leads to coincidental nucleotide matches. We show here the utility of the method by applying it to genomic sequences of Plasmodium falciparum. A single scan of chromosomes 2 and 3 of P. falciparum, using our method and no other a priori information about the sequences, reveals regions of low complexity in both telomeric and central regions, long repeats in the subtelomeric regions, and shorter repeat areas in dense coding regions. Application of the method to a recently sequenced contig of chromosome 10 that has a particularly biased base composition detects a long internal repeat more readily than does the conventional dot matrix plot. Space requirements are linear, so the method can be used on large sequences. The observed repeat patterns may be related to large-scale chromosomal organization and control of gene expression. The method has general application in detecting patterns of potential interest in newly sequenced genomic material.

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A new challenge for compression algorithms: Genetic sequences

Cited by 231 publications

References 10 publications

Compressive genomics

Compressive genomics

A New Revisited Compression Technique through Innovative Partiotion Group Binary Compression: A Novel Approach

Discovering patterns in Plasmodium falciparum genomic DNA

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