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
收藏
页码：240 / 249
页数：10
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