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A simpler analysis of Burrows–Wheeler-based compression

Haim Kaplan, Shir Landau, Elad Verbin
2007 Theoretical Computer Science  
In this paper we present a new technique for worst-case analysis of compression algorithms which are based on the Burrows-Wheeler Transform.  ...  Finally, we apply our techniques to prove a worst-case bound on the compression ratio of a compression algorithm based on the Burrows-Wheeler Transform followed by distance coding, for which worst-case  ...  We thank Giovanni Manzini for sharing with us a preliminary implementation of compression booster. The third author would like to thank Roberto Grossi for some insightful discussions.  ... 
doi:10.1016/j.tcs.2007.07.020 fatcat:ujldiywxmbdbxg7df2jost2cva

A Simpler Analysis of Burrows-Wheeler Based Compression [chapter]

Haim Kaplan, Shir Landau, Elad Verbin
2006 Lecture Notes in Computer Science  
In this paper we present a new technique for worst-case analysis of compression algorithms which are based on the Burrows-Wheeler Transform.  ...  Finally, we apply our techniques to prove a worst-case bound on the compression ratio of a compression algorithm based on the Burrows-Wheeler Transform followed by distance coding, for which worst-case  ...  We thank Giovanni Manzini for sharing with us a preliminary implementation of compression booster. The third author would like to thank Roberto Grossi for some insightful discussions.  ... 
doi:10.1007/11780441_26 fatcat:hvvhbhj66zbexnahjirvznldpa

Burrows-Wheeler compression with variable length integer codes

Peter Fenwick
2002 Software, Practice & Experience  
The final coder in Burrows-Wheeler compression is usually either an adaptive Huffman coder (for speed) or a complex of arithmetic coders for better compression.  ...  The paper also describes a "sticky Move-to-Front" modification which gives a useful improvement in compression for most files.  ...  Burrows-Wheeler compression The compression algorithm described by Burrows and Wheeler [1] differs from most compression methods in that it processes a file in blocks.  ... 
doi:10.1002/spe.484 fatcat:ya4aa6yd2jdenobegsk372iobm

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.  ...  Some of it is accordingly rather less formal in style than might otherwise be the case, as I give more personal opinions on various aspects.  ...  Burrows Wheeler or block sorting compression is based upon two quite separate transformations, a forward transformation which permutes the input data into a form which is easily compressed, and a matching  ... 
doi:10.1016/b978-012620861-0/50008-5 fatcat:bmdaqour2fea3lqzco5k5im4ym

Burrows–Wheeler compression: Principles and reflections

Peter Fenwick
2007 Theoretical Computer Science  
After a general description of the Burrows Wheeler Transform and a brief survey of recent work on processing its output, the paper examines the coding of the zero-runs from the MTF recoding stage, an aspect  ...  The paper then proposes some new interpretations and uses of the Burrows Wheeler transform, with new insights and approaches to lossless compression, perhaps including techniques from error correction.  ...  Burrows Wheeler with PPM-Conclusions This final section has described investigations into a novel combination of a Burrows Wheeler Transform with PPM compression.  ... 
doi:10.1016/j.tcs.2007.07.012 fatcat:rsifq647zngobjgifvi22nddru

A secure, lossless, and compressed Base62 encoding

Kejing He, Xiancheng Xu, Qiang Yue
2008 2008 11th IEEE Singapore International Conference on Communication Systems  
Burrows-Wheeler Transform (BWT) is used along with range coding to compress data before it is transfered to base 62 encoder.  ...  This paper presents a lossless base 62 compressed encoding method that only use alphanumeric characters to represent the original data.  ...  Burrows-Wheeler Transform (BWT) Burrows-Wheeler Transform is a reversible transformation that can make a given data more localized. BWT itself neither compress data, nor change character values.  ... 
doi:10.1109/iccs.2008.4737287 fatcat:6emj6anthvax3iryymscwymxs4

New Approach in E-mail Based Text Steganography

Kemal Tutuncu, Abdikarim Abi Hassan
2015 International Journal of Intelligent Systems and Applications in Engineering  
The members of distance matrix were compressed by following lossless compression algorithms as in written sequence; Run Length Encoding (RLE) + Burrows Wheeler Transform (BWT) + Move to Front (MTF) + Run  ...  In this study combination of lossless compression techniques and Vigenere cipher was used in the e-mail based text steganography.  ...  Apply Run Length Encoding (RLE) + Burrows Wheeler Transform (BWT) + Move to Forward (MTF) + Run Length Encoding + Arithmetic Encoding (AE) in the written order for compressing elements of R* Step5.  ... 
doi:10.18201/ijisae.05687 fatcat:6triqnub3ffl5lhlqjck5hp7je

CHIC: a short read aligner for pan-genomic references [article]

Daniel Valenzuela, Veli Mäkinen
2017 bioRxiv   pre-print
Results: We present CHIC, a short-read aligner that indexes very large and repetitive references using a hybrid technique that combines Lempel-Ziv compression with Burrows-Wheeler read aligners.  ...  Perhaps the simplest way to represent a pan-genome is to represent it as a set of sequences.  ...  Funding This work has been supported by the Academy of Finland (grant 284598 for Center of Excellence in Cancer Genetics Research).  ... 
doi:10.1101/178129 fatcat:ijpgo7hjtjalpchhv36xhtzodu

Low HRV entropy is strongly associated with myocardial infarction

Stephan Lau, Jens Haueisen, Ernst G. Schukat-Talamazzini, Andreas Voss, Matthias Goernig, Uwe Leder, Hans-R. Figulla
2006 Biomedical Engineering  
Each interval was encoded as 1 bytes8 bit in a file. The file was then compressed using Bzip2 w6x, an implementation of the Burrows-Wheeler compression.  ...  In this study, the entropy was estimated by compressing the quantized tachogram with Burrows-Wheeler compression w5x, which is one of the most efficient algorithms.  ... 
doi:10.1515/bmt.2006.033 pmid:17061935 fatcat:aq2h7cxmrfazpaumycfboyg3xy

Fixed Block Compression Boosting in FM-Indexes [article]

Juha Kärkkäinen, Simon J. Puglisi
2011 arXiv   pre-print
Our main result is a new technique called fixed block compression boosting, which is a simpler and faster alternative to optimal compression boosting and implicit compression boosting used in previous  ...  A compressed full-text self-index occupies space close to that of the compressed text and simultaneously allows fast pattern matching and random access to the underlying text.  ...  The main components of most FM-indexes are: -The Burrows-Wheeler transform (BWT) [1] : an invertible permutation of the text T .  ... 
arXiv:1104.3810v1 fatcat:5gq2hbflbzapbkiwtypoqsmwu4

A Multi GPU Read Alignment Algorithm with Model-Based Performance Optimization [chapter]

Aleksandr Drozd, Naoya Maruyama, Satoshi Matsuoka
2013 Lecture Notes in Computer Science  
We adapted Burrows Wheeler transform based index to be used with GPUs to reduce overall memory footprint.  ...  This paper describes a performance model for read alignment problem, one of the most computationally intensive tasks in bionformatics.  ...  The analysis of application behavior for the case of workload size considerably exceeding device memory proves that higher performance can me achieved by intelligent strategy for data decomposition.  ... 
doi:10.1007/978-3-642-38718-0_27 fatcat:uxgxoxrnszehpcaapgtd6chrti

Compression Of Semistructured Documents

Leo Galambos, Jan Lansky, Katsiaryna Chernik
2008 Zenodo  
There already exist a special compression text algorithms and methods for a compression of XML documents.  ...  The aim of this paper is an integration of the two approaches to achieve an optimal level of the compression ratio  ...  XBW The new XBW method is based on Burrows-Wheeler transformation [3] . Burrows-Wheeler transformation was chosen for its success in the bzip2 program [20] .  ... 
doi:10.5281/zenodo.1328998 fatcat:cpis2yy63rdfpo5g7bpjdbzl3a

An Alphabet-Friendly FM-Index [chapter]

Paolo Ferragina, Giovanni Manzini, Veli Mäkinen, Gonzalo Navarro
2004 Lecture Notes in Computer Science  
Moreover, the index design does not depend on the parameter k, which plays a role only in analysis of the space occupancy.  ...  We show that, by combining an existing compression boosting technique with the wavelet tree data structure, we are able to design a variant of the FM-index which scales well with the size of the input  ...  The Burrows-Wheeler transform In [1] Burrows and Wheeler introduced a new compression algorithm based on a reversible transformation now called the Burrows-Wheeler Transform (BWT from now on).  ... 
doi:10.1007/978-3-540-30213-1_23 fatcat:wpdpepzp6rafpnhp5gpf767sym

Parallel lossless data compression on the GPU

Ritesh A. Patel, Yao Zhang, Jason Mak, Andrew Davidson, John D. Owens
2012 2012 Innovative Parallel Computing (InPar)  
We present parallel algorithms and implementations of a bzip2-like lossless data compression scheme for GPU architectures.  ...  Our approach parallelizes three main stages in the bzip2 compression pipeline: Burrows-Wheeler transform (BWT), move-to-front transform (MTF), and Huffman coding.  ...  Acknowledgments Many thanks to Adam Herr and Shubhabrata Sengupta of Intel, and Anjul Patney and Stanley Tzeng of UC Davis.  ... 
doi:10.1109/inpar.2012.6339599 fatcat:sjwuaayrwjbatgd6f7uttjt5la

Next Generation Sequencing Data and its Compression

Bruno Carpentieri
2019 IOP Conference Series: Earth and Environment  
of generic compression tools such as gzip and bzip2 by confronting them with a specific system that was designed specifically for genomic file compression: quip.  ...  In a very short time researchers have developed hardware tools, analysis software, algorithms, private databases and infrastructures to support genomics.  ...  Acknowledgment The author thanks his student Felice D'Avino for conducting preliminary tests on the compression of FASTQ and SAM/BAM files.  ... 
doi:10.1088/1755-1315/362/1/012059 fatcat:ufnk3r4r25aq3ko275brwqxlca
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