Nongreedy Unbalanced Huffman Tree Compressor for Single and Multifasta Files

Alyami, Sultan; Huang, Chun-Hsi

doi:10.1089/cmb.2019.0249

Cited by 9 publications

(3 citation statements)

References 15 publications

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“…The run-length encoding (RLE) [ 11 ], Huffman [ 12 ], and DEFLATE were employed to compress grass wave and defect wave data. Figure 2 shows that CR of defect wave data obtained by different algorithms was higher than the ratio of grass wave data.…”

Section: Resultsmentioning

confidence: 99%

Values of Contrast-Enhanced Ultrasound in Classification and Diagnosis of Common Bile Duct and Superficial Organ Lesions under Compression Algorithm

Zhao

Qin

et al. 2021

Journal of Healthcare Engineering

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This work aimed to investigate values of contrast-enhanced ultrasound (CEUS) under DEFLATE in the classification and diagnosis of the common bile duct and superficial lymphoid lesions. 88 patients with lower common bile duct lesions and 126 patients with superficial lymphoid lesions were selected as the subjects investigated and examined by CEUS under DEFLATE to compare characteristics and diagnostic efficiency of CEUS in different types of lesions. The time-intensity curve (TIC) was for quantitative analysis on CEUS results. The results showed that there were statistically significant differences in the comparison of time to peak (TTP), area under the curve (AUC), and gradient (Grad) of common bile duct walls in patients from the malignant group ( P < 0.05), while the comparison of three indicators of patients in the benign group was not statistically remarkable ( P > 0.05). In addition, there were statistically great differences in TTP, AUC, and Grad among patients in the benign and malignant groups ( P < 0.05). The sensitivity, specificity, accuracy, and positive/negative predictive value of CEUS + ultrasound (US) in the diagnosis of benign and malignant lymph nodes were 92.83%, 87.14%, 89.54%, 91.23%, and 86.43%, respectively. The values of maximal intensity (Imax) in the reactive hyperplasia group (group A), lymphoma group (group B), and metastatic lymph nodes group (group C) were compared, showing statistical differences ( P < 0.05). The TTP and AUC of group B were higher than those of groups A and C, respectively ( P < 0.05), and the base-to-peak ascending slope (KUP) and the absolute value of the semidescending slope (KDOWN) in group C increased hugely compared to group A ( P < 0.05). It indicated that CEUS examination under DEFLATE could be applied in the qualitative diagnosis of lower common bile duct lesions and superficial lymphoid lesions, which was worthy of clinical application.

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Section: Resultsmentioning

confidence: 99%

Values of Contrast-Enhanced Ultrasound in Classification and Diagnosis of Common Bile Duct and Superficial Organ Lesions under Compression Algorithm

Zhao

Qin

et al. 2021

Journal of Healthcare Engineering

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“…We tested all DNA sequence compressors that are available and functional in 2020: dnaX [ 14 ], XM [ 15 ], DELIMINATE [ 16 ], Pufferfish [ 17 ], DNA-COMPACT [ 18 ], MFCompress [ 19 ], UHT [ 20 ], GeCo [ 21 ], GeCo2 [ 22 ], JARVIS [ 23 ], NAF [ 24 ], and NUHT [ 25 ]. We also included the relatively compact among homology search database formats: BLAST [ 26 ] and 2bit—a database format of BLAT [ 27 ].…”

Section: Resultsmentioning

confidence: 99%

Sequence Compression Benchmark (SCB) database—A comprehensive evaluation of reference-free compressors for FASTA-formatted sequences

et al. 2020

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Abstract Background Nearly all molecular sequence databases currently use gzip for data compression. Ongoing rapid accumulation of stored data calls for a more efficient compression tool. Although numerous compressors exist, both specialized and general-purpose, choosing one of them was difficult because no comprehensive analysis of their comparative advantages for sequence compression was available. Findings We systematically benchmarked 430 settings of 48 compressors (including 29 specialized sequence compressors and 19 general-purpose compressors) on representative FASTA-formatted datasets of DNA, RNA, and protein sequences. Each compressor was evaluated on 17 performance measures, including compression strength, as well as time and memory required for compression and decompression. We used 27 test datasets including individual genomes of various sizes, DNA and RNA datasets, and standard protein datasets. We summarized the results as the Sequence Compression Benchmark database (SCB database, http://kirr.dyndns.org/sequence-compression-benchmark/), which allows custom visualizations to be built for selected subsets of benchmark results. Conclusion We found that modern compressors offer a large improvement in compactness and speed compared to gzip. Our benchmark allows compressors and their settings to be compared using a variety of performance measures, offering the opportunity to select the optimal compressor on the basis of the data type and usage scenario specific to a particular application.

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“…27 Some experimental tools provide limited DNA compression: Pufferfish, 28 UHT, 29 and NUHT. 30 In addition, many FASTQ compressors can be adapted for FASTA-formatted DNA data compression: beetl, 31 DSRC, 32 Quip, 33 fastqz, 34 fqzcomp, 34 Leon, 35 LFQC, 36 KIC, 37 HARC, 38 LFastqC, 39 Minicom, 40 SPRING, 41 and FQSqueezer. 42 Specialized sequence compressors can be classified into two categories: referential and reference free.…”

Section: Sequence-compression Overviewmentioning

confidence: 99%

Efficient compression of SARS-CoV-2 genome data using Nucleotide Archival Format

Kryukov

Jin²,

Nakagawa

2022

Patterns

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Nongreedy Unbalanced Huffman Tree Compressor for Single and Multifasta Files

Cited by 9 publications

References 15 publications

Values of Contrast-Enhanced Ultrasound in Classification and Diagnosis of Common Bile Duct and Superficial Organ Lesions under Compression Algorithm

Values of Contrast-Enhanced Ultrasound in Classification and Diagnosis of Common Bile Duct and Superficial Organ Lesions under Compression Algorithm

Sequence Compression Benchmark (SCB) database—A comprehensive evaluation of reference-free compressors for FASTA-formatted sequences

Efficient compression of SARS-CoV-2 genome data using Nucleotide Archival Format

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