HADC: A Hybrid Compression Approach for DNA Sequences
In the blossoming age of Next Generation Sequencing (NGS) technologies, genome sequencing has become much easier and more affordable. The large number of enormous genomic sequences obtained demand the availability of huge storage space in order to be kept for analysis. Since the storage cost has bec...
Ausführliche Beschreibung
Autor*in: |
Sarah Elnady [verfasserIn] Sabah Sayed [verfasserIn] Akram Salah [verfasserIn] |
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E-Artikel |
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Englisch |
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2022 |
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Übergeordnetes Werk: |
In: IEEE Access - IEEE, 2014, 10(2022), Seite 106841-106848 |
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Übergeordnetes Werk: |
volume:10 ; year:2022 ; pages:106841-106848 |
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DOI / URN: |
10.1109/ACCESS.2022.3212523 |
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DOAJ028293975 |
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10.1109/ACCESS.2022.3212523 doi (DE-627)DOAJ028293975 (DE-599)DOAJ38877d0c0aa44c38b3f2cf28c5338be4 DE-627 ger DE-627 rakwb eng TK1-9971 Sarah Elnady verfasserin aut HADC: A Hybrid Compression Approach for DNA Sequences 2022 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier In the blossoming age of Next Generation Sequencing (NGS) technologies, genome sequencing has become much easier and more affordable. The large number of enormous genomic sequences obtained demand the availability of huge storage space in order to be kept for analysis. Since the storage cost has become an impediment facing biologists, there is a constant need of software that provides efficient compression of genomic sequences. Most general-purpose compression algorithms do not exploit the inherent redundancies that exist in genomic sequences which is the reason for the success and popularity of reference-based compression algorithms. In this research, a new reference-based lossless compression technique is proposed for deoxyribonucleic acid (DNA) sequences stored in FASTA format which can act as a layer above gzip compression. Several experiments were performed to evaluate this technique and the experimental results show that it is able to obtain promising compression ratios saving up to 99.9% space and reaching a gain of 80% for some plant genomes. The proposed technique also succeeds in performing the compression at acceptable time; even saving more than 50% of the time taken by ERGC in most experiments. Bioinformatics DNA sequences reference-based compression greedy alignment Electrical engineering. Electronics. Nuclear engineering Sabah Sayed verfasserin aut Akram Salah verfasserin aut In IEEE Access IEEE, 2014 10(2022), Seite 106841-106848 (DE-627)728440385 (DE-600)2687964-5 21693536 nnns volume:10 year:2022 pages:106841-106848 https://doi.org/10.1109/ACCESS.2022.3212523 kostenfrei https://doaj.org/article/38877d0c0aa44c38b3f2cf28c5338be4 kostenfrei https://ieeexplore.ieee.org/document/9912395/ kostenfrei https://doaj.org/toc/2169-3536 Journal toc kostenfrei GBV_USEFLAG_A SYSFLAG_A GBV_DOAJ GBV_ILN_11 GBV_ILN_20 GBV_ILN_22 GBV_ILN_23 GBV_ILN_24 GBV_ILN_31 GBV_ILN_39 GBV_ILN_40 GBV_ILN_60 GBV_ILN_62 GBV_ILN_63 GBV_ILN_65 GBV_ILN_69 GBV_ILN_70 GBV_ILN_73 GBV_ILN_95 GBV_ILN_105 GBV_ILN_110 GBV_ILN_151 GBV_ILN_161 GBV_ILN_170 GBV_ILN_213 GBV_ILN_230 GBV_ILN_285 GBV_ILN_293 GBV_ILN_370 GBV_ILN_602 GBV_ILN_2014 GBV_ILN_4012 GBV_ILN_4037 GBV_ILN_4112 GBV_ILN_4125 GBV_ILN_4126 GBV_ILN_4249 GBV_ILN_4305 GBV_ILN_4306 GBV_ILN_4307 GBV_ILN_4313 GBV_ILN_4322 GBV_ILN_4323 GBV_ILN_4324 GBV_ILN_4325 GBV_ILN_4335 GBV_ILN_4338 GBV_ILN_4367 GBV_ILN_4700 AR 10 2022 106841-106848 |
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10.1109/ACCESS.2022.3212523 doi (DE-627)DOAJ028293975 (DE-599)DOAJ38877d0c0aa44c38b3f2cf28c5338be4 DE-627 ger DE-627 rakwb eng TK1-9971 Sarah Elnady verfasserin aut HADC: A Hybrid Compression Approach for DNA Sequences 2022 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier In the blossoming age of Next Generation Sequencing (NGS) technologies, genome sequencing has become much easier and more affordable. The large number of enormous genomic sequences obtained demand the availability of huge storage space in order to be kept for analysis. Since the storage cost has become an impediment facing biologists, there is a constant need of software that provides efficient compression of genomic sequences. Most general-purpose compression algorithms do not exploit the inherent redundancies that exist in genomic sequences which is the reason for the success and popularity of reference-based compression algorithms. In this research, a new reference-based lossless compression technique is proposed for deoxyribonucleic acid (DNA) sequences stored in FASTA format which can act as a layer above gzip compression. Several experiments were performed to evaluate this technique and the experimental results show that it is able to obtain promising compression ratios saving up to 99.9% space and reaching a gain of 80% for some plant genomes. The proposed technique also succeeds in performing the compression at acceptable time; even saving more than 50% of the time taken by ERGC in most experiments. Bioinformatics DNA sequences reference-based compression greedy alignment Electrical engineering. Electronics. Nuclear engineering Sabah Sayed verfasserin aut Akram Salah verfasserin aut In IEEE Access IEEE, 2014 10(2022), Seite 106841-106848 (DE-627)728440385 (DE-600)2687964-5 21693536 nnns volume:10 year:2022 pages:106841-106848 https://doi.org/10.1109/ACCESS.2022.3212523 kostenfrei https://doaj.org/article/38877d0c0aa44c38b3f2cf28c5338be4 kostenfrei https://ieeexplore.ieee.org/document/9912395/ kostenfrei https://doaj.org/toc/2169-3536 Journal toc kostenfrei GBV_USEFLAG_A SYSFLAG_A GBV_DOAJ GBV_ILN_11 GBV_ILN_20 GBV_ILN_22 GBV_ILN_23 GBV_ILN_24 GBV_ILN_31 GBV_ILN_39 GBV_ILN_40 GBV_ILN_60 GBV_ILN_62 GBV_ILN_63 GBV_ILN_65 GBV_ILN_69 GBV_ILN_70 GBV_ILN_73 GBV_ILN_95 GBV_ILN_105 GBV_ILN_110 GBV_ILN_151 GBV_ILN_161 GBV_ILN_170 GBV_ILN_213 GBV_ILN_230 GBV_ILN_285 GBV_ILN_293 GBV_ILN_370 GBV_ILN_602 GBV_ILN_2014 GBV_ILN_4012 GBV_ILN_4037 GBV_ILN_4112 GBV_ILN_4125 GBV_ILN_4126 GBV_ILN_4249 GBV_ILN_4305 GBV_ILN_4306 GBV_ILN_4307 GBV_ILN_4313 GBV_ILN_4322 GBV_ILN_4323 GBV_ILN_4324 GBV_ILN_4325 GBV_ILN_4335 GBV_ILN_4338 GBV_ILN_4367 GBV_ILN_4700 AR 10 2022 106841-106848 |
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10.1109/ACCESS.2022.3212523 doi (DE-627)DOAJ028293975 (DE-599)DOAJ38877d0c0aa44c38b3f2cf28c5338be4 DE-627 ger DE-627 rakwb eng TK1-9971 Sarah Elnady verfasserin aut HADC: A Hybrid Compression Approach for DNA Sequences 2022 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier In the blossoming age of Next Generation Sequencing (NGS) technologies, genome sequencing has become much easier and more affordable. The large number of enormous genomic sequences obtained demand the availability of huge storage space in order to be kept for analysis. Since the storage cost has become an impediment facing biologists, there is a constant need of software that provides efficient compression of genomic sequences. Most general-purpose compression algorithms do not exploit the inherent redundancies that exist in genomic sequences which is the reason for the success and popularity of reference-based compression algorithms. In this research, a new reference-based lossless compression technique is proposed for deoxyribonucleic acid (DNA) sequences stored in FASTA format which can act as a layer above gzip compression. Several experiments were performed to evaluate this technique and the experimental results show that it is able to obtain promising compression ratios saving up to 99.9% space and reaching a gain of 80% for some plant genomes. The proposed technique also succeeds in performing the compression at acceptable time; even saving more than 50% of the time taken by ERGC in most experiments. Bioinformatics DNA sequences reference-based compression greedy alignment Electrical engineering. Electronics. Nuclear engineering Sabah Sayed verfasserin aut Akram Salah verfasserin aut In IEEE Access IEEE, 2014 10(2022), Seite 106841-106848 (DE-627)728440385 (DE-600)2687964-5 21693536 nnns volume:10 year:2022 pages:106841-106848 https://doi.org/10.1109/ACCESS.2022.3212523 kostenfrei https://doaj.org/article/38877d0c0aa44c38b3f2cf28c5338be4 kostenfrei https://ieeexplore.ieee.org/document/9912395/ kostenfrei https://doaj.org/toc/2169-3536 Journal toc kostenfrei GBV_USEFLAG_A SYSFLAG_A GBV_DOAJ GBV_ILN_11 GBV_ILN_20 GBV_ILN_22 GBV_ILN_23 GBV_ILN_24 GBV_ILN_31 GBV_ILN_39 GBV_ILN_40 GBV_ILN_60 GBV_ILN_62 GBV_ILN_63 GBV_ILN_65 GBV_ILN_69 GBV_ILN_70 GBV_ILN_73 GBV_ILN_95 GBV_ILN_105 GBV_ILN_110 GBV_ILN_151 GBV_ILN_161 GBV_ILN_170 GBV_ILN_213 GBV_ILN_230 GBV_ILN_285 GBV_ILN_293 GBV_ILN_370 GBV_ILN_602 GBV_ILN_2014 GBV_ILN_4012 GBV_ILN_4037 GBV_ILN_4112 GBV_ILN_4125 GBV_ILN_4126 GBV_ILN_4249 GBV_ILN_4305 GBV_ILN_4306 GBV_ILN_4307 GBV_ILN_4313 GBV_ILN_4322 GBV_ILN_4323 GBV_ILN_4324 GBV_ILN_4325 GBV_ILN_4335 GBV_ILN_4338 GBV_ILN_4367 GBV_ILN_4700 AR 10 2022 106841-106848 |
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10.1109/ACCESS.2022.3212523 doi (DE-627)DOAJ028293975 (DE-599)DOAJ38877d0c0aa44c38b3f2cf28c5338be4 DE-627 ger DE-627 rakwb eng TK1-9971 Sarah Elnady verfasserin aut HADC: A Hybrid Compression Approach for DNA Sequences 2022 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier In the blossoming age of Next Generation Sequencing (NGS) technologies, genome sequencing has become much easier and more affordable. The large number of enormous genomic sequences obtained demand the availability of huge storage space in order to be kept for analysis. Since the storage cost has become an impediment facing biologists, there is a constant need of software that provides efficient compression of genomic sequences. Most general-purpose compression algorithms do not exploit the inherent redundancies that exist in genomic sequences which is the reason for the success and popularity of reference-based compression algorithms. In this research, a new reference-based lossless compression technique is proposed for deoxyribonucleic acid (DNA) sequences stored in FASTA format which can act as a layer above gzip compression. Several experiments were performed to evaluate this technique and the experimental results show that it is able to obtain promising compression ratios saving up to 99.9% space and reaching a gain of 80% for some plant genomes. The proposed technique also succeeds in performing the compression at acceptable time; even saving more than 50% of the time taken by ERGC in most experiments. Bioinformatics DNA sequences reference-based compression greedy alignment Electrical engineering. Electronics. Nuclear engineering Sabah Sayed verfasserin aut Akram Salah verfasserin aut In IEEE Access IEEE, 2014 10(2022), Seite 106841-106848 (DE-627)728440385 (DE-600)2687964-5 21693536 nnns volume:10 year:2022 pages:106841-106848 https://doi.org/10.1109/ACCESS.2022.3212523 kostenfrei https://doaj.org/article/38877d0c0aa44c38b3f2cf28c5338be4 kostenfrei https://ieeexplore.ieee.org/document/9912395/ kostenfrei https://doaj.org/toc/2169-3536 Journal toc kostenfrei GBV_USEFLAG_A SYSFLAG_A GBV_DOAJ GBV_ILN_11 GBV_ILN_20 GBV_ILN_22 GBV_ILN_23 GBV_ILN_24 GBV_ILN_31 GBV_ILN_39 GBV_ILN_40 GBV_ILN_60 GBV_ILN_62 GBV_ILN_63 GBV_ILN_65 GBV_ILN_69 GBV_ILN_70 GBV_ILN_73 GBV_ILN_95 GBV_ILN_105 GBV_ILN_110 GBV_ILN_151 GBV_ILN_161 GBV_ILN_170 GBV_ILN_213 GBV_ILN_230 GBV_ILN_285 GBV_ILN_293 GBV_ILN_370 GBV_ILN_602 GBV_ILN_2014 GBV_ILN_4012 GBV_ILN_4037 GBV_ILN_4112 GBV_ILN_4125 GBV_ILN_4126 GBV_ILN_4249 GBV_ILN_4305 GBV_ILN_4306 GBV_ILN_4307 GBV_ILN_4313 GBV_ILN_4322 GBV_ILN_4323 GBV_ILN_4324 GBV_ILN_4325 GBV_ILN_4335 GBV_ILN_4338 GBV_ILN_4367 GBV_ILN_4700 AR 10 2022 106841-106848 |
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In the blossoming age of Next Generation Sequencing (NGS) technologies, genome sequencing has become much easier and more affordable. The large number of enormous genomic sequences obtained demand the availability of huge storage space in order to be kept for analysis. Since the storage cost has become an impediment facing biologists, there is a constant need of software that provides efficient compression of genomic sequences. Most general-purpose compression algorithms do not exploit the inherent redundancies that exist in genomic sequences which is the reason for the success and popularity of reference-based compression algorithms. In this research, a new reference-based lossless compression technique is proposed for deoxyribonucleic acid (DNA) sequences stored in FASTA format which can act as a layer above gzip compression. Several experiments were performed to evaluate this technique and the experimental results show that it is able to obtain promising compression ratios saving up to 99.9% space and reaching a gain of 80% for some plant genomes. The proposed technique also succeeds in performing the compression at acceptable time; even saving more than 50% of the time taken by ERGC in most experiments. |
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In the blossoming age of Next Generation Sequencing (NGS) technologies, genome sequencing has become much easier and more affordable. The large number of enormous genomic sequences obtained demand the availability of huge storage space in order to be kept for analysis. Since the storage cost has become an impediment facing biologists, there is a constant need of software that provides efficient compression of genomic sequences. Most general-purpose compression algorithms do not exploit the inherent redundancies that exist in genomic sequences which is the reason for the success and popularity of reference-based compression algorithms. In this research, a new reference-based lossless compression technique is proposed for deoxyribonucleic acid (DNA) sequences stored in FASTA format which can act as a layer above gzip compression. Several experiments were performed to evaluate this technique and the experimental results show that it is able to obtain promising compression ratios saving up to 99.9% space and reaching a gain of 80% for some plant genomes. The proposed technique also succeeds in performing the compression at acceptable time; even saving more than 50% of the time taken by ERGC in most experiments. |
abstract_unstemmed |
In the blossoming age of Next Generation Sequencing (NGS) technologies, genome sequencing has become much easier and more affordable. The large number of enormous genomic sequences obtained demand the availability of huge storage space in order to be kept for analysis. Since the storage cost has become an impediment facing biologists, there is a constant need of software that provides efficient compression of genomic sequences. Most general-purpose compression algorithms do not exploit the inherent redundancies that exist in genomic sequences which is the reason for the success and popularity of reference-based compression algorithms. In this research, a new reference-based lossless compression technique is proposed for deoxyribonucleic acid (DNA) sequences stored in FASTA format which can act as a layer above gzip compression. Several experiments were performed to evaluate this technique and the experimental results show that it is able to obtain promising compression ratios saving up to 99.9% space and reaching a gain of 80% for some plant genomes. The proposed technique also succeeds in performing the compression at acceptable time; even saving more than 50% of the time taken by ERGC in most experiments. |
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|
score |
7.3987417 |