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A four-stage algorithm for updating a Burrows–Wheeler transform
2009
Theoretical Computer Science
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We present a four-stage algorithm that updates the Burrows-Wheeler Transform of a text T , when this text is modified. ...
The Burrows-Wheeler Transform is used by many text compression applications and some self-index data structures. ...
Conclusion We proposed a four-stage algorithm that updates the Burrows-Wheeler Transform of a text T whenever standard edit operations are modifying T . ...
doi:10.1016/j.tcs.2009.07.016
fatcat:7epl7gq3lzatnf75hc7jb47qai
Higher Compression from Burrows-Wheeler Transform for DNA Sequence
2017
International Journal of Computer Applications
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General Terms Algorithms Keywords DNA sequence compression, Burrows-Wheeler Transform, BWT and genome. ...
In this paper, the Burrows-Wheeler Transform (BWT) based approaches are explored to compress the biological sequences. ...
METHODS 2.1 Burrows-Wheeler Transform The Burrows-Wheeler Transform (BWT) was developed by Michael Burrows and David J. Wheeler in 1994 [3] . ...
doi:10.5120/ijca2017915261
fatcat:n7bl3a5e2ffyjkoedhv2ch36qq
Burrows—Wheeler Compression
[chapter]
2003
Lossless Compression Handbook
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The material of this chapter, while quoting extensively from other work, is in part a summary of my own experience and thoughts in working with the Burrows-Wheeler compression algorithm. ...
Sorting Algorithm, a generalisation of the Burrows-Wheeler transform. ...
It appears that the Burrows-Wheeler transform is almost unique; it
, who without much effort achieved a compression of 2.52bpc on the Calgary Corpus in a Burrows-Wheeler compressor with no MTF stage. ...
doi:10.1016/b978-012620861-0/50008-5
fatcat:bmdaqour2fea3lqzco5k5im4ym
The impact of lossless image compression to radiographs
2006
Medical Imaging 2006: PACS and Imaging Informatics
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compression algorithm (BWCA) with respect to image content and origin. ...
The effect of lossy image compression is frequently analyzed with respect to images from a certain modality supporting a certain diagnosis. ...
For decompression, the four stages are executed in reverse order using the inverse schemes each time: 1. the so called Burrows-Wheeler transform (BWT) performs a permutation of the input symbols [21] ...
doi:10.1117/12.651697
fatcat:bxc7fmjjtrhl3oo2efllc6gcei
Dynamic extended suffix arrays
2010
Journal of Discrete Algorithms
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This algorithm is based on a recent four-stage algorithm developed for dynamic Burrows-Wheeler Transforms (BWT). ...
For minimizing the space complexity, we are sampling the Suffix Array, a technique used in BWT-based compressed indexes. ...
Acknowledgments The corresponding author would like to thank Gene Myers for being more than a constant source of inspiration. ...
doi:10.1016/j.jda.2009.02.007
fatcat:3rwijo4skraghjcclg3eyurkwq
An Efficient Data Compression Approach based on Entropic Codingfor Network Devices with Limited Resources
2019
European Journal of Electrical Engineering and Computer Science
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The proposed approachis based on entropic Arithmetic coding, Run-length encoding, Burrows-wheeler transform and Move-to-front encoding. ...
This paper introduces MediCompress, a lightweight lossless data compression approach for irretrievable data like those from the medical or astronomy fields. ...
Burrows-Wheeler Transform Transformed from Burrows-Wheeler's principle is to rearrange a string of characters into a series of similar characters. ...
doi:10.24018/ejece.2019.3.5.121
fatcat:v4e3fk7fwzhltdfvab4mrj272u
Second step algorithms in the Burrows-Wheeler compression algorithm
2002
Software, Practice & Experience
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In this paper we fix our attention on the second step algorithms of the Burrows-Wheeler compression algorithm, which in the original version is the Move To Front transform. ...
Then we propose a new algorithm that yields a better compression ratio than the previous ones. ...
Jesper Larsson for the source code of the suffix tree creation algorithm and John Carpinelli, Alistair Moffat, Radford Neal, Wayne Salamonsen, Lang Stuiver and Ian Witten for the source code of the arithmetic ...
doi:10.1002/spe.426
fatcat:dtaufcgadrbh7cxvvnzdxqgwau
Enhancing Dictionary Based Preprocessing for Better Text Compression
English
2014
International Journal of Computer Trends and Technology
English
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For efficient compression a dictionary based transformation algorithm is also developed. ...
The popular block sorting lossless Burrows Wheeler Compression Algorithm (BWCA) is implemented along with one proposed method. ...
BWCA comprises of 4 stages which include Burrows Wheeler Transform (BWT),Global Structure Transformation (GST), Run Length Encoding (RLE) and Entropy Coder. ...
doi:10.14445/22312803/ijctt-v9p102
fatcat:crncn2xgtbbkvjqdqjjhyl4mfe
Enhancing Dictionary Based Preprocessing For Better Text Compression
[article]
2014
arXiv
pre-print
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For efficient compression a dictionary based transformation algorithm is also developed. ...
The popular block sorting lossless Burrows Wheeler Compression Algorithm (BWCA) is implemented along with one proposed method. ...
BWCA comprises of 4 stages which include Burrows Wheeler Transform (BWT),Global Structure Transformation (GST), Run Length Encoding (RLE) and Entropy Coder. ...
arXiv:1403.4714v1
fatcat:mpt77yaibvctjnib7x2xttpz6m
Indeterminate String Factorizations and Degenerate Text Transformations
2017
Mathematics in Computer Science
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The Burrows-Wheeler transformation computes a permutation of a string of letters over an alphabet, and is well-suited to compression-related applications due to its invertability and data clustering properties ...
A core computation in Burrows-Wheeler type transforms is the linear sorting of all conjugates of the input string-we achieve this in the degenerate case with lex-extension ordering. ...
In [35] , a four-stage algorithm is presented that updates the BWT(T ) when the text T is modified into T according to standard edit operations-insertion, deletion, and substitution of a character or ...
doi:10.1007/s11786-016-0285-x
fatcat:dpic7m34xnctxlsraukgtngx6m
Optimal and efficient time series classification with burrows-wheeler transform and spectral window based transformation
2018
Periodicals of Engineering and Natural Sciences (PEN)
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In this proposed technique, with the help of the Burrows-Wheeler Transform (BWT), primarily frequency domain based data transformation is carried out. ...
Therefore time series classification is taken as a significant research problem for the examining as well as identifying the time series dataset. ...
Burrows-wheeler transform (BWT) for frequency domain In this research, to do the frequency domain analysis, Burrows-Wheeler Transform (BWT) is presented [22] .The BWT considers a block of data as well ...
doi:10.21533/pen.v6i1.275
fatcat:inrvfzwxzfeaffl2quwjlhu3se
MSAC: Compression of multiple sequence alignment files
[article]
2017
bioRxiv
pre-print
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It is based on a generalisation of the positional Burrows-Wheeler transform for non-binary alphabets. MSAC handles FASTA, as well as Stockholm files. ...
Results: We propose a novel compression algorithm, MSAC (Multiple Sequence Alignment Compressor), designed especially for aligned data. ...
supported by Polish National Science Centre under the project DEC-2015/17/B/ST6/01890 and performed using the infrastructure supported by POIG.02.03.01-24-099/13 grant: 'GeCONiI-Upper Silesian Center for ...
doi:10.1101/240341
fatcat:ncawasrybrhflad5qlguypmbpq
Faster suffix sorting
2007
Theoretical Computer Science
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We propose a fast and memory-efficient algorithm for lexicographically sorting the suffixes of a string, a problem that has important applications in data compression as well as string matching. ...
For input size n, our algorithm operates in only two integer arrays of size n, and has worst-case time complexity O(n log n). ...
The Burrows-Wheeler Transform [5] is a process that has the capability of concentrating repetitions in a string, which facilitates data compression. ...
doi:10.1016/j.tcs.2007.07.017
fatcat:hp4z2fauxfhjxkqiqbdhimfnz4
ECG Signal Compression Based on Burrows-Wheeler Transformation and Inversion Ranks of Linear Prediction
2007
IEEE Transactions on Biomedical Engineering
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However, the recently introduced Burrows-Wheeler Transformation has not been completely investigated. In this paper, we investigate the lossless compression of ECG signals. ...
We show that when compressing ECG signals, utilization of linear prediction, Burrows-Wheeler Transformation, and inversion ranks yield better compression gain in terms of weighted average bit per sample ...
Tabus for supplying him the ECG data used in their work and fruitful discussion on the data formats used in the MIT-BIH database. ...
doi:10.1109/tbme.2006.888820
pmid:17355052
fatcat:q46cuxvapzaipa5fzdusyo7hr4
Fast Parallel Suffix Array on the GPU
[chapter]
2015
Lecture Notes in Computer Science
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We also demonstrate the effectiveness of our implementations in a Burrows-Wheeler transform and a parallel FM index for pattern searching. ...
The first, skew, makes algorithmic improvements to the previous work of Deo and Keely to achieve a speedup of 1.45x over their work. ...
We would like to acknowledge Mrinal Deo for providing their paper's original data, Vitaly Osipov for sharing his paper's source code for comparision, and both Jason Mak and Carl Yang for feedback on early ...
doi:10.1007/978-3-662-48096-0_44
fatcat:q3dlbm6enrhrboksyni4y5pxqy
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