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### 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.  ...

### Circular pattern matching with k mismatches

Panagiotis Charalampopoulos, Tomasz Kociumaka, Solon P. Pissis, Jakub Radoszewski, Wojciech Rytter, Juliusz Straszyński, Tomasz Waleń, Wiktor Zuba
2020 Journal of computer and system sciences (Print)
This is the circular pattern matching with k mismatches (k-CPM) problem.  ...  a r t i c l e i n f o a b s t r a c t We consider the circular pattern matching with k mismatches (k-CPM) problem in which one is to compute the minimal Hamming distance of every length-m substring of  ...  Circular Pattern Matching with k Mismatches can be solved in O(min(nk, n + n m k 4 )) time and O(m) space. table.  ...

### Circular Pattern Matching with k Mismatches [article]

Panagiotis Charalampopoulos, Tomasz Kociumaka, Solon P. Pissis, Jakub Radoszewski, Wojciech Rytter, Juliusz Straszyński, Tomasz Waleń, Wiktor Zuba
2020 arXiv   pre-print
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.  ...

### New layout strategies with improved matching performance

Chengming He, Xin Dai, Hanqing Xing, Degang Chen
Among these three techniques, the central symmetry patterns have the best-reported matching performance for Manhattan structures; the circular-symmetry patterns have the best theoretical matching performance  ...  Three layout strategies with improved matching performance are reviewed and summarized.  ...  N th order circular symmetry pattern The circular symmetry layout pattern is initially proposed for 1-1 matching between two devices.  ...

### Approximate Online Matching of Circular Strings [chapter]

Tommi Hirvola, Jorma Tarhio
2014 Lecture Notes in Computer Science
From this algorithm, we derive several sublinear methods for approximate online matching of circular strings. The applicability of the new algorithms is demonstrated with practical experiments.  ...  Recently a fast algorithm based on the BNDM algorithm has been presented for exact matching of circular strings.  ...  matching of circular strings with k errors.  ...

### 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  ...  string matching with k-mismatches.  ...

### sRNA Profiler: A User-Focused Interface for Small RNA Mapping and Profiling

Charith Raj Adkar-Purushothama, Pavithran Sridharan Iyer, Teruo Sano, Jean-Pierre Perreault
2021 Cells
In order to overcome this constraint, and to help the research community in general, in this study, a python-based pattern matching interface was developed so as to be able to both profile and map sRNAs  ...  on a circular genome.  ...  To summarize, two length k strings α and β match approximately with at most δ mismatches if and only if the Hamming weight of b(α)·b(β) is at most k − δ.  ...

### Subject Index

2007 Journal of Discrete Algorithms
with mismatches Parameterized matching with mismatches, 135 Pattern-matching A simple fast hybrid pattern-matching algorithm, 682 Periodicity Two-pattern strings II-frequency of occurrence and substring  ...  particle filters, 455 Path coupling Path coupling without contraction, 280 PATRICIA tree Text indexing with errors, 662 Pattern matching Parameterized matching with mismatches, 135; Searching for  ...

### Generalised Implementation for Fixed-Length Approximate String Matching under Hamming Distance and Applications

2015 2015 IEEE International Parallel and Distributed Processing Symposium Workshop
Approximate string matching is the problem of finding all factors of a text t of length n with a distance at most k from a pattern x of length m ≤ n.  ...  Fixed-length approximate string matching is the problem of finding all factors of a text t of length n with a distance at most k from any factor of length h of a pattern x of length m ≤ n, where h ≤ m.  ...  That is, D[m, j] ≤ k denotes an occurrence of x at the ending position j − 1 in t with at most k mismatches.  ...

### Fast String Matching with Mismatches

R.A. Baezayates, G.H. Gonnet
1994 Information and Computation
We describe and analyze three simple and fast algorithms on the average for solving the problem of string matching with a bounded number of mismatches.  ...  Introduction The problem of string matching with k mismatches consists of nding all occurrences of a pattern of length m in a text of length n such that in at most k positions the text and the pattern  ...  , with at most k mismatches.  ...

### Effect of surface texture and geometry on spoof surface plasmon dispersion

Shun-Hui Yang
2008 Optical Engineering: The Journal of SPIE
We then compare the specific cases of circular versus rectangular textured surfaces and observe that the plasmon modes are less tightly bound in the former case.  ...  For example, we find that SPPs are less tightly bound to a surface patterned with circular holes compared to a surface comprising square/rectangular holes due to a smaller momentum mismatch.  ...  The size of the circular holes ͑R=88 nm, D=350 nm͒ is chosen to match the plasmon frequency of the rectangular patterned surface ͑a=b=150 nm, D =350 nm͒.  ...

### Camera focusing based on fringe pattern matching

Peter J. Bryanston-Cross, Zuobin Wang
1997 Applied Optics
A method of camera focusing based on fringe pattern matching is presented. In the method, the variance of the mismatch function is used as a focus measure.  ...  The experimental results show that the focus measure based on fringe pattern matching performs well in peak sharpness, monotonicity, and noise sensitivity and that it has a better performance in noise  ...  In fringe pattern matching, the mismatch function for the fringe patterns with vertical fringes can be calculated by 8, 9 f k ͑t͒ ϭ 1 MN ͚ mϭ1 M ͚ nϭ1 N ͓I k ͑m, n͒ Ϫ I k ͑m, n ϩ t͔͒ 2 , k ϭ 0, 1, 2,  ...

### gkmSVM: an R package for gapped-kmer SVM

Mahmoud Ghandi, Morteza Mohammad-Noori, Narges Ghareghani, Dongwon Lee, Levi Garraway, Michael A. Beer
2016 Bioinformatics
This package supports several sequence kernels, including: gkmSVM, kmer-SVM, mismatch kernel and wildcard kernel.  ...  We then build a k-mer tree using all the mismatch patterns assigned to each pass and use that to prune the DFS search in that pass.  ...  In practice, we generate all the possible patterns of mismatches (all the binary strings of length L with at most D ones) and assign each mismatch pattern d to the pass p that gives the minimum cost: p  ...

### Identification of Fingerprints using Circular String Approximation for Mobile Devices

Oluwole I. Ajala, Costas S. Iliopoulos, Mujibur R. Khan
2017 Communiation Papers of the 2017 Federated Conference on Computer Science and Information Systems
stage and then match the fingerprint image with stored images using algorithms for approximate circular string matching.  ...  Responding to this issue, this report proposes a novel pattern matching technique that caters for orientation differences in fingerprints, by implementing a pre-matching stage called the orientation identification  ...  It takes into consideration that there could be errors or mismatches from unnecessary characters in both texts and patterns, insertions and deletions (k differences).  ...