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

*
String Processing and Information Retrieval
*

In this paper we focus on

doi:10.1007/978-3-540-75530-2_24
dblp:conf/spire/RussoNO07
fatcat:ft7ntvf57fbdtilni7nhcduvjm
*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. ...##
###
Subject Index

2004
*
Journal of Discrete Algorithms
*

pattern

doi:10.1016/s1570-8667(04)00076-0
fatcat:3igwdxr5pba53eev4y6a2jzgie
*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 ...##
###
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 ...

##
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Approximate String Matching with Compressed Indexes

2009
*
Algorithms
*

In this paper we focus on

doi:10.3390/a2031105
fatcat:y5co44757jgi5eabwlslyutddu
*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*. ...##
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Lempel-Ziv Compression in a Sliding Window

2017
*
Annual Symposium on Combinatorial Pattern Matching
*

We present new algorithms for the sliding window

doi:10.4230/lipics.cpm.2017.15
dblp:conf/cpm/BilleCFG17
fatcat:3i727sm6rfabrg5noezebkco4a
*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*. ...##
###
Dictionary-Based Data Compression
[chapter]

2008
*
Encyclopedia of Algorithms
*

This technique originated in two theoretical papers of

doi:10.1007/978-0-387-30162-4_108
fatcat:o3szv6nhtrcufii5b7a6rkoebu
*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. ...##
###
Dictionary-Based Data Compression
[chapter]

2016
*
Encyclopedia of Algorithms
*

This technique originated in two theoretical papers of

doi:10.1007/978-1-4939-2864-4_108
fatcat:mmpcgzwxa5capiloipjqmxv2ea
*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. ...##
###
A Vital Approach to compress the Size of DNA Sequence using LZW (Lempel-Ziv-Welch) with Fixed Length Binary Code and Tree Structure

2012
*
International Journal of Computer Applications
*

This paper proposes a new hybrid algorithm is used to

doi:10.5120/6065-8193
fatcat:bwdiplzeqvhhxcr6i4x3vfghly
*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. ...##
###
Pattern-matching and text-compression algorithms

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. ...

##
###
Pattern Matching and Text Compression Algorithms
[chapter]

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. ...

##
###
Indexing Highly Repetitive Collections
[chapter]

2012
*
Lecture Notes in Computer Science
*

In this short survey we briefly describe the progress made along three research lines to address the problem:

doi:10.1007/978-3-642-35926-2_29
fatcat:j5hhapqyvbcszbcbqdozzt63t4
*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. ...##
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Differential Ziv-Lempel Text Compression
[chapter]

1996
*
J.UCS The Journal of Universal Computer Science
*

We describe a novel text compressor which combines

doi:10.1007/978-3-642-80350-5_49
fatcat:uq3e4y3pj5cnxnr6yoi2nyq2sa
*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. ...##
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Lempel–Ziv Data Compression on Parallel and Distributed Systems

2011
*
Algorithms
*

We present a survey of results concerning

doi:10.3390/a4030183
fatcat:dc7r2mbxkvha7i4u5vygffdxra
*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. ...##
###
Lempel-Ziv Data Compression on Parallel and Distributed Systems

2011
*
2011 First International Conference on Data Compression, Communications and Processing
*

We present a survey of results concerning

doi:10.1109/ccp.2011.11
dblp:conf/ccp/Agostino11
fatcat:oc2rfggfnfhkxa62vodgstvram
*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. ...##
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An implementable lossy version of the Lempel-Ziv algorithm. I. Optimality for memoryless sources

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. ...

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