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A four-stage algorithm for updating a Burrows–Wheeler transform

M. Salson, T. Lecroq, M. Léonard, L. Mouchard
2009 Theoretical Computer Science  
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

Rexline S., Aju Richard, Trujilla Lobo
2017 International Journal of Computer Applications  
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]

Peter Fenwick
2003 Lossless Compression Handbook  
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

Thomas M. Lehmann, Jürgen Abel, Claudia Weiss, Steven C. Horii, Osman M. Ratib
2006 Medical Imaging 2006: PACS and Imaging Informatics  
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

M. Salson, T. Lecroq, M. Léonard, L. Mouchard
2010 Journal of Discrete Algorithms  
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

Elie Fute Tagne, Hugues Marie Kamdjou, Alain Bertrand Bomgni, Armand Nzeukou
2019 European Journal of Electrical Engineering and Computer Science  
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

Sebastian Deorowicz
2002 Software, Practice & Experience  
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

R. R. Baruah, V Deka, M. P. Bhuyan
2014 International Journal of Computer Trends and Technology  
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]

R. R. Baruah, V.Deka, M. P. Bhuyan
2014 arXiv   pre-print
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

Jacqueline W. Daykin, Bruce Watson
2017 Mathematics in Computer Science  
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

T. Karthikeyan
2018 Periodicals of Engineering and Natural Sciences (PEN)  
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]

Sebastian Deorowicz, Joanna Walczyszyn, Agnieszka Debudaj-Grabysz
2017 bioRxiv   pre-print
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

N. Jesper Larsson, Kunihiko Sadakane
2007 Theoretical Computer Science  
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

Ziya Arnavut
2007 IEEE Transactions on Biomedical Engineering  
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]

Leyuan Wang, Sean Baxter, John D. Owens
2015 Lecture Notes in Computer Science  
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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