CBSTD: A Cloud Based Symbol Table Driven DNA Compression Algorithm

Majumder, Annwesha Banerjee; Gupta, Somsubhra

doi:10.1007/978-981-10-3953-9_45

Cited by 4 publications

(5 citation statements)

References 9 publications

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“…We summarize in table 4 the D(q) result calculation with qϵ]-40, 40[. According to the figure 5, the figure 6 and the figure 7 we observe that : The D(q) values for all FCGR images, Image FD FCGR 1 1.7957 FCGR 2 1.7613 FCGR 3 1.7545 FCGR 4 1.7292 FCGR 5 1.7289 FCGR 6 1.7223 FCGR 7 1.6775 FCGR 8 1.4569 decreasing with increasing q values and this evident in multifractal nature. The D(q) curve of FCGR1 is almost a horizontal line.…”

Section: Fractal and Multifractal Analysis Of The Homo Sapienschromosome 22mentioning

confidence: 92%

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Involving FCGR images in studying fractality and multifractality in human chromosome 22 and bacteria complete genome

2021

IJATCSE

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The frequency chaos game representation (FCGR) is a simple yet powerful visualization method of DNA sequences. It provides the possibility of representing genomes by images, revealing in such a way different fractal structures. In this paper, we perform a fractal and multifractal analysis of Human chromosome 22 and some complete genomes based on the FGCR image. We used the fractal dimension (FD) and the multifractality degree (ΔDq) to characterize and distinguish genomes. First, we construct the FCGR image with different orders of human chromosome 22. Next, we calculate the fractal dimension, the general dimension spectrum and the multifractal spectrum of each FCGR image using the box-counting method. Then, we examine the FCGR image fractal and multifractal characteristics impact on highlighting the existence of repetitive DNA sequences in human chromosome 22. We also observe the relationship between fractality and multifractality. After that, we apply this study to bacteria completes genomes and C.elegans chromosome I. The obtained results show that the multifractal spectra of all organisms studied are multifractal-like and chromosome 22 strong multifractality proves its richness of repetitive sequences. Also, we observed that with the increasing the FCGR order value, the multifractality grows and the fractal dimension lessens. Finally, by assigning to each sequence a point in two-dimensional space (FD, ΔDq), we obtained three classes of genomes. We can easily distinguish the human chromosome 22 from other genomes and Bacteria are almost close in the spaces (FD, ΔDq).

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Section: Fractal and Multifractal Analysis Of The Homo Sapienschromosome 22mentioning

confidence: 92%

“…This DNA by its appearance, its composition and its complexity, contains preciously the elementary details of each organism. Microscopically, the DNA reveals chains of characters constituted by the bases adenine (A), thymine (T), cytosine (C) and guanine (G) [1]. DNA molecule structure is described by the double helix.…”

Section: Introductionmentioning

confidence: 99%

Involving FCGR images in studying fractality and multifractality in human chromosome 22 and bacteria complete genome

2021

IJATCSE

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“…This biomolecule not only contains the genetic information required for the functioning and development of all living beings but also aids in medical treatments in the detection of the risk for certain diseases, in the diagnosis of genetic disorders, and the identification of a specific individual [4,5]. Around three billion characters and more than 23 pairs of chromosomes are in the human genome, in a gram of soil there is 40 million bacterial cells, and certain amphibian species can even have more than 100 billion nucleotides [3,6]. With the emergent evolution in DNA sequencing technology, the volume of biological data has increased significantly.…”

Section: Introductionmentioning

confidence: 99%

“…Recently, a cloud-based symbol table driven DNA compression algorithm (CBSTD) using R language was proposed in [6]. In this technique, the entire DNA sequence is subdivided into blocks (each block contains four bases), and then looked into which category it belongs.…”

Section: Introductionmentioning

confidence: 99%

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A New Lossless DNA Compression Algorithm Based on A Single-Block Encoding Scheme

2020

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With the emergent evolution in DNA sequencing technology, a massive amount of genomic data is produced every day, mainly DNA sequences, craving for more storage and bandwidth. Unfortunately, managing, analyzing and specifically storing these large amounts of data become a major scientific challenge for bioinformatics. Therefore, to overcome these challenges, compression has become necessary. In this paper, we describe a new reference-free DNA compressor abbreviated as DNAC-SBE. DNAC-SBE is a lossless hybrid compressor that consists of three phases. First, starting from the largest base (Bi), the positions of each Bi are replaced with ones and the positions of other bases that have smaller frequencies than Bi are replaced with zeros. Second, to encode the generated streams, we propose a new single-block encoding scheme (SEB) based on the exploitation of the position of neighboring bits within the block using two different techniques. Finally, the proposed algorithm dynamically assigns the shorter length code to each block. Results show that DNAC-SBE outperforms state-of-the-art compressors and proves its efficiency in terms of special conditions imposed on compressed data, storage space and data transfer rate regardless of the file format or the size of the data.

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One-Bit DNA Compression Algorithm

Mansouri

Yuan

2018

Lecture Notes in Computer Science

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CBSTD: A Cloud Based Symbol Table Driven DNA Compression Algorithm

Cited by 4 publications

References 9 publications

Involving FCGR images in studying fractality and multifractality in human chromosome 22 and bacteria complete genome

Involving FCGR images in studying fractality and multifractality in human chromosome 22 and bacteria complete genome

A New Lossless DNA Compression Algorithm Based on A Single-Block Encoding Scheme

One-Bit DNA Compression Algorithm

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