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Approximate String Matching with Lempel-Ziv Compressed Indexes [chapter]

Luís M. S. Russo, Gonzalo Navarro, Arlindo L. Oliveira
String Processing and Information Retrieval  
In this paper we focus on indexed approximate string matching (ASM), which is of great interest, say, in computational biology applications.  ...  We show that a Lempel-Ziv index can be seen as an extension of the classical q-samples index.  ...  A Hybrid Lempel-Ziv Index The following lemma describes the way we combine previous results to search using a Lempel-Ziv index. Lemma 4. Let A and B be strings such that 0 < ed(A, B) ≤ k.  ... 
doi:10.1007/978-3-540-75530-2_24 dblp:conf/spire/RussoNO07 fatcat:ft7ntvf57fbdtilni7nhcduvjm

Subject Index

2004 Journal of Discrete Algorithms  
pattern matching Indexing text using the Ziv-Lempel trie, 87; Prac- tical and flexible pattern matching over Ziv- Lempel compressed text, 347 Compressed text Indexing text using the Ziv-Lempel trie  ...  over Ziv- Lempel compressed text, 347 LZ78 Practical and flexible pattern matching over Ziv- Lempel compressed text, 347 LZW Practical and flexible pattern matching over Ziv- Lempel compressed text  ... 
doi:10.1016/s1570-8667(04)00076-0 fatcat:3igwdxr5pba53eev4y6a2jzgie

Subject Index

2003 Journal of Discrete Algorithms  
strings, 357 Work Cooperative computing with fragmentable and mergeable groups, 211 Ziv-Lempel Regular expression searching on compressed text, 423 Ziv-Lempel compression Approximate string matching on  ...  , 357 Dynamic programming Approximate string matching on Ziv-Lempel compressed text, 313 Edit distance Approximate string matching on Ziv-Lempel compressed text, 313; Applying an edit distance  ... 
doi:10.1016/s1570-8667(03)00075-3 fatcat:icg7if3uingibmjwy2mjud4rwe

Approximate String Matching with Compressed Indexes

Luís M. Russo, Gonzalo Navarro, Arlindo Oliveira, Pedro Morales
2009 Algorithms  
In this paper we focus on indexed approximate string matching (ASM), which is of great interest, say, in bioinformatics.  ...  We study ASM algorithms for Lempel-Ziv compressed indexes and for compressed suffix trees/arrays. Most compressed self-indexes belong to one of these classes.  ...  Hierarchical Approximate String Matching Bidirectional Compressed Indexes Our final algorithm can be implemented over any bidirectional index.  ... 
doi:10.3390/a2031105 fatcat:y5co44757jgi5eabwlslyutddu

Lempel-Ziv Compression in a Sliding Window

Philip Bille, Patrick Hagge Cording, Johannes Fischer, Inge Li Gørtz, Marc Herbstritt
2017 Annual Symposium on Combinatorial Pattern Matching  
We present new algorithms for the sliding window Lempel-Ziv (LZ77) problem and the approximate rightmost LZ77 parsing problem.  ...  rightmost matching problem.  ...  Introduction The Lempel-Ziv parsing (LZ77) [36] of a string is a key component in data compression, detecting regularities in strings, pattern matching, and string indexing.  ... 
doi:10.4230/lipics.cpm.2017.15 dblp:conf/cpm/BilleCFG17 fatcat:3i727sm6rfabrg5noezebkco4a

Dictionary-Based Data Compression [chapter]

Travis Gagie, Giovanni Manzini
2008 Encyclopedia of Algorithms  
This technique originated in two theoretical papers of Ziv and Lempel [15, 16] and gained popularity in the "80s" with the introduction of the Unix tool compress (1986) and of the gif image format (  ...  transforms one string T into another Compressed Full-Text Indexing Given a text T, the problem of compressed full-text indexing is defined as the task of building an index for T that takes space proportional  ...  Dictionary Matching: In dictionary matching one is given a dictionary D of strings p 1 ;:::;p d to be preprocessed.  ... 
doi:10.1007/978-0-387-30162-4_108 fatcat:o3szv6nhtrcufii5b7a6rkoebu

Dictionary-Based Data Compression [chapter]

Travis Gagie, Giovanni Manzini
2016 Encyclopedia of Algorithms  
This technique originated in two theoretical papers of Ziv and Lempel [15, 16] and gained popularity in the "80s" with the introduction of the Unix tool compress (1986) and of the gif image format (  ...  transforms one string T into another Compressed Full-Text Indexing Given a text T, the problem of compressed full-text indexing is defined as the task of building an index for T that takes space proportional  ...  Dictionary Matching: In dictionary matching one is given a dictionary D of strings p 1 ;:::;p d to be preprocessed.  ... 
doi:10.1007/978-1-4939-2864-4_108 fatcat:mmpcgzwxa5capiloipjqmxv2ea

A Vital Approach to compress the Size of DNA Sequence using LZW (Lempel-Ziv-Welch) with Fixed Length Binary Code and Tree Structure

Nishad PM, R. Manicka Chezian
2012 International Journal of Computer Applications  
This paper proposes a new hybrid algorithm is used to compress DNA sequence, the algorithm is designed by combining the fixed length binary code with the LZW (Lempel-Ziv-Welch) compression algorithm.  ...  Assigning a new binary code for each pattern in the dictionary using a binary tree, and the sequence is replaced binary code for the longest match in the dictionary while compression.  ...  Ziv, with later modifications by Terry A. Welch [9] . Lempel-Ziv-Welch (LZW) [9] this algorithm proposed by Welch in 1984.  ... 
doi:10.5120/6065-8193 fatcat:bwdiplzeqvhhxcr6i4x3vfghly

Pattern-matching and text-compression algorithms

Maxime Crochemore, Thierry Lecroq
1996 ACM Computing Surveys  
With the Levenshtein distance (or edit distance) the problem is known as the approximate string matching with k differences. Approximate string searching is a lively domain of research.  ...  With the Hamming distance related to the number of mismatches between the pattern and its approximate occurrences, the problem is also called approximate string matching with k mismatches.  ... 
doi:10.1145/234313.234331 fatcat:l35fbobetbdezblncuj2egwflu

Pattern Matching and Text Compression Algorithms [chapter]

Thierry Lecroq
2014 Computing Handbook, Third Edition  
With the Levenshtein distance (or edit distance) the problem is known as the approximate string matching with k differences. Approximate string searching is a lively domain of research.  ...  With the Hamming distance related to the number of mismatches between the pattern and its approximate occurrences, the problem is also called approximate string matching with k mismatches.  ... 
doi:10.1201/b16812-18 fatcat:4hclurhe3rfjricyfpxe3bggvq

Indexing Highly Repetitive Collections [chapter]

Gonzalo Navarro
2012 Lecture Notes in Computer Science  
In this short survey we briefly describe the progress made along three research lines to address the problem: compressed suffix arrays, grammar compressed indexes, and Lempel-Ziv compressed indexes.  ...  The need to index and search huge highly repetitive sequence collections is rapidly arising in various fields, including computational biology, software repositories, versioned collections, and others.  ...  n) Lempel-Ziv compression [16] O(s log n) O(m 2 h + m log n) O(t h) the nodes labeled by a given nonterminal containing a primary occurrence are found.  ... 
doi:10.1007/978-3-642-35926-2_29 fatcat:j5hhapqyvbcszbcbqdozzt63t4

Differential Ziv-Lempel Text Compression [chapter]

Peter Fenwick
1996 J.UCS The Journal of Universal Computer Science  
We describe a novel text compressor which combines Ziv-Lempel compression and arithmetic coding with a form of vector quantisation.  ...  The resulting compressor resembles an LZ-77 compressor, but with no explicit phrase lengths or coding for literals.  ...  The Ziv-Lempel parser is based on a recently-developed string matching algorithm [Fenwick and Gutmann, 1994] , a description of which is included in an Appendix to this paper.  ... 
doi:10.1007/978-3-642-80350-5_49 fatcat:uq3e4y3pj5cnxnr6yoi2nyq2sa

Lempel–Ziv Data Compression on Parallel and Distributed Systems

Sergio De Agostino
2011 Algorithms  
We present a survey of results concerning Lempel-Ziv data compression on parallel and distributed systems, starting from the theoretical approach to parallel time complexity to conclude with the practical  ...  Storer's extension for image compression is also discussed.  ...  Lempel-Ziv Data Compression Lempel-Ziv compression is a dictionary-based technique.  ... 
doi:10.3390/a4030183 fatcat:dc7r2mbxkvha7i4u5vygffdxra

Lempel-Ziv Data Compression on Parallel and Distributed Systems

Sergio De Agostino
2011 2011 First International Conference on Data Compression, Communications and Processing  
We present a survey of results concerning Lempel-Ziv data compression on parallel and distributed systems, starting from the theoretical approach to parallel time complexity to conclude with the practical  ...  Storer's extension for image compression is also discussed.  ...  Lempel-Ziv Data Compression Lempel-Ziv compression is a dictionary-based technique.  ... 
doi:10.1109/ccp.2011.11 dblp:conf/ccp/Agostino11 fatcat:oc2rfggfnfhkxa62vodgstvram

An implementable lossy version of the Lempel-Ziv algorithm. I. Optimality for memoryless sources

I. Kontoyiannis
1999 IEEE Transactions on Information Theory  
Index Terms-Fixed database, Lempel-Ziv, lossy data compression, universal source coding.  ...  A new lossy variant of the Fixed-Database Lempel-Ziv coding algorithm for encoding at a fixed distortion level is proposed, and its asymptotic optimality and universality for memoryless sources (with respect  ...  ACKNOWLEDGMENT The author gratefully acknowledges several interesting conversations on the subject with A. Dembo and T. Cover, and also wishes to thank W.  ... 
doi:10.1109/18.796370 fatcat:lyprbb5pyrdczhbrzcvvuec23m
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