A New Approach of Protein Sequence Compression using Repeat Reduction and ASCII Replacement

Haque, Shahina

doi:10.9790/0661-1054651

Cited by 2 publications

(3 citation statements)

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“…Exploiting the "dictionary" is taken into consideration in the methods proposed in [10,21,22]. In [21], the ProtCompSecS method is presented, which considers the encoding of protein sequences in connection with their annotated secondary structure information.…”

Section: Protein Sequence Compressionmentioning

confidence: 99%

“…CaBLASTP is the combination of a dictionary-based compression algorithm and a sequence alignment algorithm. In [10], a dictionary-based scheme is proposed, which is based on random or repeated protein sequence reduction and ASCII replacement.…”

Section: Protein Sequence Compressionmentioning

confidence: 99%

“…Proteins play a fundamental role in all organisms, due to their involvement in the control of their development [9][10][11]. Protein sequences are represented by a 20-symbol alphabet of amino acids.…”

Section: Protein Sequence Compressionmentioning

confidence: 99%

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A Survey on Data Compression Methods for Biological Sequences

2016

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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.

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