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Multiple filtration and approximate pattern matching

P. A. Pevzner, M. S. Waterman
1995 Algorithmica  
In the case q = m the problem coincides with the classical approximate string matching with k mismatches problem.  ...  In the case q = m the substring matching problem yields the approximate string matching problem with k-mismatches.  ...  We are grateful to William Chang, Udi Manber, and Gene Myers for useful suggestions. We are indebted to both referees for many helpful comments.  ... 
doi:10.1007/bf01188584 fatcat:npihqvjupnaj7k3zmdryfv4j54

Scalable Algorithms for String Kernels with Inexact Matching

Pavel P. Kuksa, Pai-Hsi Huang, Vladimir Pavlovic
2008 Neural Information Processing Systems  
We present a new family of linear time algorithms for string comparison with mismatches under the string kernels framework.  ...  In particular, on large alphabets and under loose mismatch constraints our algorithms are several orders of magnitude faster than the existing algorithms for string comparison under the mismatch similarity  ...  string kernels, leading to very efficient and simple algorithms that could benefit many applications.  ... 
dblp:conf/nips/KuksaHP08 fatcat:occ5nshtsrgefejh3kmc7ujxpq

BDD-BASED ANALYSIS OF GAPPED q-GRAM FILTERS

MARC FONTAINE, STEFAN BURKHARDT, JUHA KÄRKKÄINEN
2005 International Journal of Foundations of Computer Science  
Our results apply to the k-mismatches problem, i.e. approximate string matching with Hamming distance.  ...  Recently, there has been a surge of interest in gapped q-gram filters for approximate string matching.  ...  Representing Match-Mismatch-Patterns with BDDs Let A and B be two strings of length l. We call the bit-string p(A, B) ∈ {0, 1} l the match-mismatch-pattern of the two strings.  ... 
doi:10.1142/s0129054105003698 fatcat:vmc5f3sz4fcd7e5pmrqxomqc5u

Parameterized Matching [chapter]

Moshe Lewenstein
2008 Encyclopedia of Algorithms  
of t with at most k mismatched mapped-elements.  ...  matching with threshold k, up till an O(log |t|) factor (this can be achieved by reducing approximate parameterized matching to the problem by using a binary search on the k's).  ...  Given two equal-length strings s and s ′ , with mp ≤ k mismatch pairs.  ... 
doi:10.1007/978-0-387-30162-4_282 fatcat:yj4letyrdrewra7awa2q6yaqdq

Generalized Similarity Kernels for Efficient Sequence Classification [chapter]

Pavel P. Kuksa, Imdadullah Khan, Vladimir Pavlovic
2012 Proceedings of the 2012 SIAM International Conference on Data Mining  
In this work we propose a novel computational framework that uses general similarity metrics S(·, ·) and distance-preserving embeddings with string kernels to improve sequence classification.  ...  We show that it is possible to retain computational efficiency of string kernels while using this more "precise" measure of similarity.  ...  Spectrum/Mismatch and General Similarity Kernels In this section we will first discuss sequence matching with spectrum/mismatch kernels and then introduce general similarity string kernels as their generalization  ... 
doi:10.1137/1.9781611972825.75 dblp:conf/sdm/KuksaKP12 fatcat:edt3mqnss5bsnbxo5pqunwtpci

A new approach to text searching

R. A. Baeza-Yates, G. H. Gonnet
1989 Proceedings of the 12th annual international ACM SIGIR conference on Research and development in information retrieval - SIGIR '89  
We introduce a family of simple and fast algorithms for solving the classical string matching problem, string matching with don't care symbols and complement symbols, and multiple patterns.  ...  In addition we solve the same problems allowing up to k mismatches.  ...  Figure 4 :Figure 5 : 45 Pattern Matching with at most k mismatches (simpler version). String Matching with at most k mismatches.  ... 
doi:10.1145/75334.75352 dblp:conf/sigir/Baeza-YatesG89 fatcat:yzxr5nwz7rf4zai65ynfq7xqsy

Approximate Parameterized Matching [chapter]

Carmit Hazay, Moshe Lewenstein, Dina Sokol
2004 Lecture Notes in Computer Science  
of t with at most k mismatched mapped elements.  ...  Parameterized matching is the problem of finding all parameterized matches of a pattern string p in a text t, and approximate parameterized matching is the problem of finding at each location a bijection  ...  A simple and well-known fact is that: OBSERVATION 1. s and s parameterize match if and only if they have the same predecessor string.  ... 
doi:10.1007/978-3-540-30140-0_38 fatcat:7p27rtlxvzfdrn7rl2pye65hpy

Approximate parameterized matching

Carmit Hazay, Moshe Lewenstein, Dina Sokol
2007 ACM Transactions on Algorithms  
of t with at most k mismatched mapped elements.  ...  Parameterized matching is the problem of finding all parameterized matches of a pattern string p in a text t, and approximate parameterized matching is the problem of finding at each location a bijection  ...  A simple and well-known fact is that: OBSERVATION 1. s and s parameterize match if and only if they have the same predecessor string.  ... 
doi:10.1145/1273340.1273345 fatcat:yenuutsh6nbrlpkfahwef5dl4m

Fast algorithms for approximate circular string matching

Carl Barton, Costas S Iliopoulos, Solon P Pissis
2014 Algorithms for Molecular Biology  
Conclusions: We present two fast average-case algorithms for approximate circular string matching with k-mismatches; and show that they also perform very well in practice.  ...  Based on our solution for the exact case, we present two fast average-case algorithms for approximate circular string matching with k-mismatches, under the Hamming distance model, requiring time O(n) for  ...  The authors would like to warmly thank the "Reviewer #1" and the "Reviewer #2" whose meticulous comments were beyond the call of duty. Author details  ... 
doi:10.1186/1748-7188-9-9 pmid:24656145 pmcid:PMC4234210 fatcat:6npbh4o5hrcwzjeqe6iblpek2y

IUPACpal: efficient identification of inverted repeats in IUPAC-encoded DNA sequences

Hayam Alamro, Mai Alzamel, Costas S Iliopoulos, Solon P Pissis, Steven Watts
2021 BMC Bioinformatics  
We present IUPACPAL, an exact tool for efficient identification of inverted repeats in IUPAC-encoded DNA sequences allowing also for potential mismatches and gaps in the inverted repeats.  ...  Inverted repeats are found in both prokaryotic and eukaryotic genomes and they have been linked with countless possible functions.  ...  We refer to a string as a gapped inverted repeat within k mismatches when it can be expressed in the form WG W R with δ H (W , W R ) ≤ k .  ... 
doi:10.1186/s12859-021-03983-2 pmid:33549041 fatcat:sdgpfwclqfburouojrhzuqlysa

Intelligent Predictive String Search Algorithm

Dipendra Gurung, Udit Kr. Chakraborty, Pratikshya Sharma
2016 Procedia Computer Science  
It does not involve complex computations and uses simple rules during a match or mismatch of a pattern character.  ...  With the advent of the internet and the huge amount of text processing associated with information mining, string search algorithms have gained importance.  ...  The main goal of string matching algorithms is to increase efficiency by reducing the number of comparisons and increase the length of shifts in case of a mismatch.  ... 
doi:10.1016/j.procs.2016.03.116 fatcat:gl6ntke5ljctzja7yko7tm4hwe

Subject Index

2007 Journal of Discrete Algorithms  
matching, 514; Regular ex- pression constrained sequence alignment, 647 Pattern matching with mismatches Parameterized matching with mismatches, 135 Pattern-matching A simple fast hybrid pattern-matching  ...  errors, 662 Pattern matching Parameterized matching with mismatches, 135; Searching for a set of correlated patterns, 149; Efficient one-dimensional real scaled matching, 205; Generalized function  ... 
doi:10.1016/s1570-8667(07)00076-7 fatcat:wfqxglrznfb6do3wyittd5pfbi

Approximate String Matching using a Bidirectional Index [article]

Gregory Kucherov, Kamil Salikhov, Dekel Tsur
2015 arXiv   pre-print
We study strategies of approximate pattern matching that exploit bidirectional text indexes, extending and generalizing ideas of Lam et al.  ...  on efficient search schemes, and finally, provide experimental computations supporting the superiority of our strategies.  ...  Let A be a non-simple string of weight k and length k + 1.  ... 
arXiv:1310.1440v3 fatcat:r4s3ammfzzcc3opce5nppscsu4

Circular Pattern Matching with k Mismatches [chapter]

Panagiotis Charalampopoulos, Tomasz Kociumaka, Solon P. Pissis, Jakub Radoszewski, Wojciech Rytter, Juliusz Straszyński, Tomasz Waleń, Wiktor Zuba
2019 Lecture Notes in Computer Science  
This is the circular pattern matching with k mismatches (k-CPM) problem.  ...  The k-mismatch problem consists in computing the Hamming distance between a pattern P of length m and every length-m substring of a text T of length n, if this distance is no more than k.  ...  This is the circular pattern matching with k mismatches (k-CPM) problem.  ... 
doi:10.1007/978-3-030-25027-0_15 fatcat:z6sytp7b7nc3xkykuvus6xhz3m

Spatial Representation for Efficient Sequence Classification

Pavel P. Kuksa, Vladimir Pavlovic
2010 2010 20th International Conference on Pattern Recognition  
We present a general, simple feature representation of sequences that allows efficient inexact matching, comparison and classification of sequential data.  ...  The new representation leads to discovery of very efficient algorithms for string comparison, independent of the alphabet size.  ...  matching and comparison can be performed more efficiently.  ... 
doi:10.1109/icpr.2010.1159 dblp:conf/icpr/KuksaP10 fatcat:jagnesjq7vgpjpqw7btja7dtje
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