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Information 2016, 7(4), 56; doi:10.3390/info7040056

A Survey on Data Compression Methods for Biological Sequences

Institute of Electronics and Informatics Engineering of Aveiro/Department of Electronics, Telecommunications and Informatics (IEETA/DETI), University of Aveiro, 3810-193 Aveiro, Portugal
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Author to whom correspondence should be addressed.
Academic Editor: Khalid Sayood
Received: 27 June 2016 / Revised: 23 September 2016 / Accepted: 29 September 2016 / Published: 14 October 2016
(This article belongs to the Special Issue Multimedia Information Compression and Coding)
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Abstract

The ever increasing growth of the production of high-throughput sequencing data poses a serious challenge to the storage, processing and transmission of these data. As frequently stated, it is a data deluge. Compression is essential to address this challenge—it reduces storage space and processing costs, along with speeding up data transmission. In this paper, we provide a comprehensive survey of existing compression approaches, that are specialized for biological data, including protein and DNA sequences. Also, we devote an important part of the paper to the approaches proposed for the compression of different file formats, such as FASTA, as well as FASTQ and SAM/BAM, which contain quality scores and metadata, in addition to the biological sequences. Then, we present a comparison of the performance of several methods, in terms of compression ratio, memory usage and compression/decompression time. Finally, we present some suggestions for future research on biological data compression. View Full-Text
Keywords: protein sequence; DNA sequence; reference-free compression; reference-based compression; FASTA; Multi-FASTA; FASTQ; SAM; BAM protein sequence; DNA sequence; reference-free compression; reference-based compression; FASTA; Multi-FASTA; FASTQ; SAM; BAM
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This is an open access article distributed under the Creative Commons Attribution License which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. (CC BY 4.0).

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MDPI and ACS Style

Hosseini, M.; Pratas, D.; Pinho, A.J. A Survey on Data Compression Methods for Biological Sequences. Information 2016, 7, 56.

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