Search Results - Myer's bit-parallel algorithm

Row-wise Tiling for the Myers’ Bit-Parallel Approximate String Matching Algorithm

Authors: Kimmo Fredriksson

Source: Lecture Notes in Computer Science ISBN: 9783540201779

Access URL: https://link.springer.com/10.1007/978-3-540-39984-1_6
https://rd.springer.com/chapter/10.1007/978-3-540-39984-1_6
https://dblp.uni-trier.de/db/conf/spire/spire2003.html#Fredriksson03
https://link.springer.com/chapter/10.1007%2F978-3-540-39984-1_6

Thread-cooperative, bit-parallel computation of Levenshtein distance on GPU

Authors: Chacón de San Baldomero, Alejandro Marco-Sola, Santiago

Source: Recercat. Dipósit de la Recerca de Catalunya
instname
Recercat: Dipósit de la Recerca de Catalunya
Varias* (Consorci de Biblioteques Universitáries de Catalunya, Centre de Serveis Científics i Acadèmics de Catalunya)

Subject Terms: Myers' algorithm, GPU, CUDA, SIMD

Access URL: http://hdl.handle.net/2072/449312
https://hdl.handle.net/2072/449312

Explaining and extending the bit-parallel approximate string matching algorithm of Myers

Authors: Heikki Hyyrö The Pennsylvania State University CiteSeerX Archives

Contributors: Heikki Hyyrö The Pennsylvania State University CiteSeerX Archives

Source: http://www.cs.uta.fi/~helmu/pubs/A2001-10.pdf.

File Description: application/pdf

Relation: http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.65.61

Availability: http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.65.61
http://www.cs.uta.fi/~helmu/pubs/A2001-10.pdf

Theoretical Analysis of Edit Distance Algorithms: To what extent have the techniques for theoretical analysis of edit distance algorithms achieved their goals?

Authors: MEDVEDEV, PAUL

Source: Communications of the ACM; Dec2023, Vol. 66 Issue 12, p64-71, 8p

Subject Terms: ALGORITHMS, COMPUTER science

A BIT-PARALLEL DYNAMIC PROGRAMMING ALGORITHM SUITABLE FOR DNA SEQUENCE ALIGNMENT.

Authors: KIMURA, KOUICHI KOIKE, ASAKO NAKAI, KENTA

Source: Journal of Bioinformatics & Computational Biology. Aug2012, Vol. 10 Issue 4, p1250002-1-1250002-15. 15p. 4 Diagrams, 1 Graph.

Subject Terms: *DYNAMIC programming, *ALGORITHMS, *NUCLEOTIDE sequence, *BIOINFORMATICS, *COMPUTATIONAL biology, *GENOMES, *SEQUENCE alignment

Row-wise tiling for the Myers' bit-parallel approximate string matching algorithm

Authors: Kimmo Fredriksson The Pennsylvania State University CiteSeerX Archives

Contributors: Kimmo Fredriksson The Pennsylvania State University CiteSeerX Archives

Source: http://www.cs.uku.fi/~fredriks/pub/papers/spire03a.pdf.

File Description: application/pdf

Relation: http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.107.4959; http://www.cs.uku.fi/~fredriks/pub/papers/spire03a.pdf

Availability: http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.107.4959
http://www.cs.uku.fi/~fredriks/pub/papers/spire03a.pdf

Row-wise tiling for the Myers' bit-parallel approximate string matching algorithm

Authors: Kimmo Fredriksson The Pennsylvania State University CiteSeerX Archives

Contributors: Kimmo Fredriksson The Pennsylvania State University CiteSeerX Archives

Source: http://www.cs.joensuu.fi/~kfredrik/pub/papers/spire03a.ps.

File Description: application/postscript

Relation: http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.1.8210; http://www.cs.joensuu.fi/~kfredrik/pub/papers/spire03a.ps

Availability: http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.1.8210
http://www.cs.joensuu.fi/~kfredrik/pub/papers/spire03a.ps

Bit-parallel sequence-to-graph alignment.

Authors: Rautiainen, Mikko Mäkinen, Veli Marschall, Tobias

Source: Bioinformatics. Oct2019, Vol. 35 Issue 19, p3599-3607. 9p.

Subject Terms: *DE Bruijn graph, *GRAPH algorithms, *SEQUENCE alignment, *GEOMETRIC vertices, *ERROR correction (Information theory)

Practical algorithms for biological sequence analysis : methods and applications

Authors: Retha, Ahmad Pissis, Solon Iliopoulos, Costas

Contributors: Retha, Ahmad Pissis, Solon Iliopoulos, Costas

Subject Terms: 004

Access URL: https://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.789185

Quantum Linear Algorithm for Edit Distance Using the Word QRAM Model

Authors: Equi, Massimo de Griend, Arianne Meijer-van Mäkinen, Veli

Index Terms: Quantum Physics, Computer Science - Computational Complexity, Computer Science - Data Structures and Algorithms, 81P68, E.1, E.4, F.1.3, F.2.2, text

URL: http://arxiv.org/abs/2112.13005

Bit-parallel approximate string matching algorithms with transposition

Authors: Hyyrö, Heikki¹ heikki.hyyro@cs.uta.fi

Source: Journal of Discrete Algorithms. Jun2005, Vol. 3 Issue 2-4, p215-229. 15p.

Subject Terms: Algorithms, Foundations of arithmetic, Matching theory, Combinatorics

Filtros para a busca e extração de padrões aproximados em cadeias biológicas

Filter Algorithms for Approximate Patterns Matching and Extraction from Biological Strings

Authors: Soares Neto, Domingos

Thesis Advisors: Soares, Jose Augusto Ramos

Subject Terms: algoritmos bit-paralelos, algoritmos de filtragem, approximate string matching, árvores dos sufixos, bit-parallel algorithms, busca aproximada de padrões, extração de padrões, filter algorithms, motifs, patterns extraction, q-gramas, q-grams, suffix array, suffix tree, vetor dos sufixos

File Description: application/pdf

Availability: http://www.teses.usp.br/teses/disponiveis/45/45134/tde-19102009-002745/

Study of Bit-Parallel Approximate Parameterized String Matching Algorithms

Authors: Rajesh Prasad Suneeta Agarwal

Source: Communications in Computer and Information Science ISBN: 9783642035463

Access URL: https://link.springer.com/chapter/10.1007%2F978-3-642-03547-0_4
https://rd.springer.com/chapter/10.1007/978-3-642-03547-0_4
http://ui.adsabs.harvard.edu/abs/2009coco.book...26P/abstract
https://link.springer.com/10.1007/978-3-642-03547-0_4
https://dblp.uni-trier.de/db/conf/ic3/ic3-2009.html#PrasadA09

Hardware-Algorithm Codesign for Fast and Energy Efficient Approximate String Matching on FPGA for Computational Biology

Authors: Venkateshwarlu Yellaswamy, Gudur Sidharth, Maheshwari Swati, Bhardwaj et al.

Source: 2022 44th Annual International Conference of the IEEE Engineering in Medicine & Biology Society (EMBC). :87-90

Subject Terms: 0301 basic medicine, 03 medical and health sciences, Computers, 0202 electrical engineering, electronic engineering, information engineering, Computational Biology, Conservation of Energy Resources, 02 engineering and technology, 7. Clean energy, Algorithms, Software

Access URL: https://pubmed.ncbi.nlm.nih.gov/36086088

New Bit-Parallel Indel-Distance Algorithm

Authors: Yoan J. Pinzón Heikki Hyyrö Ayumi Shinohara

Source: Lecture Notes in Computer Science ISBN: 9783540259206

Access URL: http://www.shino.ecei.tohoku.ac.jp/~ayumi/papers/WEA2005.pdf

Bit-parallel approximate string matching algorithms with transposition

Authors: Gonzalo Navarro The Pennsylvania State University CiteSeerX Archives

Contributors: Gonzalo Navarro The Pennsylvania State University CiteSeerX Archives

Source: http://www.dcc.uchile.cl/~gnavarro/ps/cpm02.2.pdf.

File Description: application/pdf

Relation: http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.636.2903; http://www.dcc.uchile.cl/~gnavarro/ps/cpm02.2.pdf

Availability: http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.636.2903
http://www.dcc.uchile.cl/~gnavarro/ps/cpm02.2.pdf

Thread-cooperative, bit-parallel computation of Levenshtein distance on GPU

Authors: Chacón, Alejandro Marco-Sola, Santiago

Subject Terms: SIMD, GPU, CUDA, Myers' algorithm

File Description: application/pdf

Relation: Ministerio de Ciencia e Innovación TIN2011-28689-C02-01; ICS : International Conference on Supercomputing; 2014; https://ddd.uab.cat/record/131865; urn:10.1145/2597652.2597677; urn:oai:ddd.uab.cat:131865; urn:scopus_id:84903764622; urn:wos_id:000380995600012

Availability: https://ddd.uab.cat/record/131865

Bit-Parallel Witnesses and Their Applications to Approximate String Matching.

Authors: Heikki Hyyrö Gonzalo Navarro

Source: Algorithmica; Jan2005, Vol. 41 Issue 3, p203-231, 37p

Subject Terms: ALGORITHMS, WITNESSES, COMBINATORICS, LEGAL evidence, IDENTIFICATION

A survey of sequence-to-graph mapping algorithms in the pangenome era.

Authors: Cui, Yingbo Peng, Chenchen Xia, Zeyu et al.

Source: Genome Biology; 5/22/2025, Vol. 26 Issue 1, p1-25, 25p

Improving the bit-parallel NFA of Baeza-Yates and Navarro for approximate string matching

Authors: Hyyrö, Heikki¹ heikki.hyyro@cs.uta.fi

Source: Information Processing Letters. Nov2008, Vol. 108 Issue 5, p313-319. 7p.

Subject Terms: *ALGORITHMS, *DYNAMIC programming, *INTEGER programming, VECTOR algebra