Genome Compression: An Image-Based Approach

被引：0

作者：

Kredens, Kelvin Vieira ^{[1
]}

Martins, Juliano Vieira ^{[1
]}

Dordal, Osmar Betazzi ^{[1
]}

Scalabrin, Edson Emilio ^{[1
]}

Herai, Roberto Hiroshi ^{[2
]}

Avila, Braulio Coelho ^{[1
]}

机构：

[1] Pontifical Catholic Univ Parana PUCPR, Grad Program Comp Sci PPGIa, Curitiba, Parana, Brazil

[2] Pontifical Catholic Univ Parana PUCPR, Grad Program Hlth Sci PPGCS, Curitiba, Parana, Brazil

来源：

ARTIFICIAL INTELLIGENCE AND SOFT COMPUTING (ICAISC 2018), PT II | 2018年 / 10842卷

关键词：

Data compression; Genome compression; Assembled genomic sequence; Lossless compression; Image file format;

D O I：

10.1007/978-3-319-91262-2_22

中图分类号：

TP18 [人工智能理论];

学科分类号：

081104 ; 0812 ; 0835 ; 1405 ;

摘要：

With the advent of Next Generation Sequencing Technologies, it has been possible to reduce the cost and time of genome sequencing. Thus, there was a significant increase in demand for genomes that were assembled daily. This demand requires more efficient techniques for storing and transmitting genomic data. In this research, we discussed the horizontal compression of lossless genomic sequences, using two image formats, WEBP, and FLIF. For this, the genomic sequence is transformed into a matrix of colored pixels, where an RGB color is assigned to each symbol of the A, T, C, G alphabet at a position x-y. The WEBP format showed the best data-rate saving (76.15%, SD= 0.84) when compared to FLIF. In addition, we compared the data-rate savings of two specialized DELIMINATE and MPCompress genomic data compression tools with WEBP. The results obtained show that the WEBP is close to DELIMINATE (76.03%, SD = 2.54%) and MFCompress (76.97%). SD = 1.36%). Finally, we suggest using WEBP for genomic data compression.

引用

页码：240 / 249

页数：10

共 50 条

[31] An Image-Based Approach to Variational Path Synthesis of Linkages
Deshpande, Shrinath
Purwar, Anurag
JOURNAL OF COMPUTING AND INFORMATION SCIENCE IN ENGINEERING, 2021, 21 (02)
[32] An Image-Based Approach to Visual Feature Space Analysis
Schreck, Tobias
Schneidewind, Joern
Keim, Daniel A.
WSCG 2008, COMMUNICATION PAPERS, 2008, : 223 - +
[33] An Image-Based Approach for Defect Detection on Decorative Sheets
Zhou, Boyu
He, Xin
Zhou, Zhongyi
Le, Xinyi
NEURAL INFORMATION PROCESSING (ICONIP 2018), PT IV, 2018, 11304 : 659 - 670
[34] Image-based biomimetic approach to reconstruction of the temporomandibular joint
Feinberg, SE
Hollister, SJ
Halloran, JW
Chu, TMG
Krebsbach, PH
CELLS TISSUES ORGANS, 2001, 169 (03) : 309 - 321
[35] An image-based approach to interactive crease extraction and rendering
Barakat, S.
Tricoche, X.
ICCS 2010 - INTERNATIONAL CONFERENCE ON COMPUTATIONAL SCIENCE, PROCEEDINGS, 2010, 1 (01): : 1703 - 1712
[36] An Image-Based Approach for Stochastic Volumetric and Procedural Details
Gilet, G.
Dischler, J-M.
COMPUTER GRAPHICS FORUM, 2010, 29 (04) : 1411 - 1419
[37] Image-Based Prognostics Using Deep Learning Approach
Aydemir, Gurkan
Paynabar, Kamran
IEEE TRANSACTIONS ON INDUSTRIAL INFORMATICS, 2020, 16 (09) : 5956 - 5964
[38] AN IMAGE-BASED APPROACH FOR THE ARCHITECTURAL MODELING OF PAST STATES
Stefani, C.
Busayarat, C.
Renaudin, N.
De Luca, L.
Veron, P.
Florenzano, M.
4TH ISPRS INTERNATIONAL WORKSHOP 3D-ARCH 2011: 3D VIRTUAL RECONSTRUCTION AND VISUALIZATION OF COMPLEX ARCHITECTURES, 2011, 38-5 (W16): : 397 - 404
[39] A Simple Image-based Object Velocity Estimation Approach
Chu, Hung-Chi
Yang, Hao
2014 IEEE 11TH INTERNATIONAL CONFERENCE ON NETWORKING, SENSING AND CONTROL (ICNSC), 2014, : 102 - 107
[40] An image-based approach for building fuzzy color spaces
Mengibar-Rodriguez, Miriam
Chamorro-Martinez, Jesus
INFORMATION SCIENCES, 2022, 616 : 577 - 592

← 1 2 3 4 5 →