short-paper

Improving the Sequence Alignment Method by Quantum Multi-Pattern Recognition

Authors:

Konstantinos Prousalis,

Nikos KonofaosAuthors Info & Claims

SETN '18: Proceedings of the 10th Hellenic Conference on Artificial Intelligence

Article No.: 50, Pages 1 - 4

https://doi.org/10.1145/3200947.3201041

Published: 09 July 2018 Publication History

Get Access

Abstract

A dot matrix approach for sequence alignment is combined with a known quantum multi-pattern recognition method in order to improve the problem of sequence alignment. This dot matrix technique allows the application of some quantum computing principles on the pattern recognition problems like those used in the Grover's algorithm. When the recognized patterns exceed the limit of the 1/3 of the overall patterns, the multi-pattern recognition is accomplished simultaneously with the probability of 100%. The contribution concerns the way that the adopted quantum pattern recognition algorithm is applied speeding up the sequence alignment process. An example application demonstrates the effectiveness of the proposed method. String alignments isn't an essential task only in bioinformatics, but also in calculating the edit distance cost between strings in a natural language or in financial data.

References

[1]

Zhou R. & Ding Q. 2008. Quantum pattern recognition with probability 100%. Int. J. Theor. Phys., 47, 5 (2008), 1278--1285.

Crossref

Google Scholar

[2]

Neigovzen R., et al. 2009. Quantum Pattern Recognition With Liquid State NMR. Phys. Rev. A, 79 (2009) 042321.

Crossref

Google Scholar

[3]

Schützhold R. 2002. Pattern recognition on a quantum computer, Phys. Rev. A. 67 (2002) 062311.

Crossref

Google Scholar

[4]

Fard E.R., Aghayar K. & Amniat-Talab M. 2018. Quantum pattern recognition with multi-neuron interactions. Quantum Inf. Process 17 (2018) 42.

Digital Library

Google Scholar

[5]

Smith T. & Waterman M. 1981. Identification of common molecular subsequences, J. Mol. Biol., 147 (1981) 195--197.

Crossref

Google Scholar

[6]

Needleman S. & Wunsch C. A general method applicable to the search for similarities in the amino acid sequence of two proteins. Journal of Molecular Biology. 48 (1970) 443--453.

Google Scholar

[7]

Pinkse P. W. H., et al. 2013. Quantum Pattern Recognition. In 2013 Conference on Lasers and Electro-Optics - International Quantum Electronics Conference, (Optical Society of America, 2013), paper IA_3_6.

Google Scholar

[8]

Grover L.K. 1996. A fast quantum mechanical algorithm for database search. In Proceedings of 28th Annual ACM Symposium on the Theory of Computing, (1996) 212.

Digital Library

Google Scholar

Cited By

View all

Nałęcz-Charkiewicz KCharkiewicz KNowak R(2024)Quantum computing in bioinformatics: a systematic review mappingBriefings in Bioinformatics10.1093/bib/bbae39125:5Online publication date: 14-Aug-2024
https://doi.org/10.1093/bib/bbae391
Corts RAlachiotis N(2023)A Survey of Processing Systems for Phylogenetics and Population GeneticsACM Transactions on Reconfigurable Technology and Systems10.1145/358803316:3(1-27)Online publication date: 20-Jun-2023
https://dl.acm.org/doi/10.1145/3588033
De R(2022)Quantum Accelerated Pattern Matching for Genome Sequencing in Complex RNA Secondary Structures2022 IEEE International Conference on Quantum Computing and Engineering (QCE)10.1109/QCE53715.2022.00139(842-843)Online publication date: Sep-2022
https://doi.org/10.1109/QCE53715.2022.00139
Show More Cited By

Index Terms

Improving the Sequence Alignment Method by Quantum Multi-Pattern Recognition

Recommendations

Quantum algorithm for multiple alignment of amino acid sequences
MCBC'09: Proceedings of the 10th WSEAS international conference on Mathematics and computers in biology and chemistry

The alignment of genome sequences or amino acid sequences is one of fundamental operations for the study of life. Usual computational complexity for the multiple alignment of N sequences with common length L by dynamic programming is O(L^N). This ...
Photonic scheme of quantum phase estimation for quantum algorithms via quantum dots
Abstract
Various quantum algorithms depend on quantum phase estimation (QPE) as basic blocks or main subroutines to leverage superposition and entanglement during quantum computations. The QPE algorithm estimates the unknown phase of an eigenvalue ...
Quantum algorithm for preparing the ground state of a physical system through multi-step quantum resonant transitions
Abstract
We present a quantum algorithm for preparing the ground state of a physical system by using a multi-step quantum resonant transition (QRT) method. We construct a sequence of intermediate Hamiltonians to reach the system Hamiltonian, and then, ...

Comments

Information & Contributors

Information

Published In

SETN '18: Proceedings of the 10th Hellenic Conference on Artificial Intelligence

July 2018

339 pages

ISBN:9781450364331

DOI:10.1145/3200947

Permission to make digital or hard copies of all or part of this work for personal or classroom use is granted without fee provided that copies are not made or distributed for profit or commercial advantage and that copies bear this notice and the full citation on the first page. Copyrights for components of this work owned by others than ACM must be honored. Abstracting with credit is permitted. To copy otherwise, or republish, to post on servers or to redistribute to lists, requires prior specific permission and/or a fee. Request permissions from [email protected]

In-Cooperation

EETN: Hellenic Artificial Intelligence Society
UOP: University of Patras
University of Thessaly: University of Thessaly, Volos, Greece

Publisher

Association for Computing Machinery

New York, NY, United States

Publication History

Published: 09 July 2018

Permissions

Request permissions for this article.

Request Permissions

Check for updates

Author Tags

Qualifiers

Short-paper
Research
Refereed limited

Conference

SETN '18

SETN '18: 10th Hellenic Conference on Artificial Intelligence

July 9 - 12, 2018

Patras, Greece

Contributors

Other Metrics

View Article Metrics

Bibliometrics & Citations

Bibliometrics

Article Metrics

7
Total Citations
View Citations
107
Total Downloads

Downloads (Last 12 months)10
Downloads (Last 6 weeks)1

Reflects downloads up to 07 Jan 2025

Other Metrics

View Author Metrics

Citations

Cited By

View all

Nałęcz-Charkiewicz KCharkiewicz KNowak R(2024)Quantum computing in bioinformatics: a systematic review mappingBriefings in Bioinformatics10.1093/bib/bbae39125:5Online publication date: 14-Aug-2024
https://doi.org/10.1093/bib/bbae391
Corts RAlachiotis N(2023)A Survey of Processing Systems for Phylogenetics and Population GeneticsACM Transactions on Reconfigurable Technology and Systems10.1145/358803316:3(1-27)Online publication date: 20-Jun-2023
https://dl.acm.org/doi/10.1145/3588033
De R(2022)Quantum Accelerated Pattern Matching for Genome Sequencing in Complex RNA Secondary Structures2022 IEEE International Conference on Quantum Computing and Engineering (QCE)10.1109/QCE53715.2022.00139(842-843)Online publication date: Sep-2022
https://doi.org/10.1109/QCE53715.2022.00139
Zhu HLiu TWang C(2021)A One-Round Quantum Mutual Authenticated Key Agreement Protocol with Semi-Honest Server Using Three-Particle Entangled StatesInternational Journal of Theoretical Physics10.1007/s10773-021-04716-0Online publication date: 20-Jan-2021
https://doi.org/10.1007/s10773-021-04716-0
Zhu DZhu HWang ZZhang Y(2021)Three‐level quantum satellite communication framework and its applicationsInternational Journal of Satellite Communications and Networking10.1002/sat.1392Online publication date: 14-Jan-2021
https://doi.org/10.1002/sat.1392
Zhu HWang LZhang Y(2020)An efficient quantum identity authentication key agreement protocol without entanglementQuantum Information Processing10.1007/s11128-020-02887-z19:10Online publication date: 16-Oct-2020
https://doi.org/10.1007/s11128-020-02887-z
Zhu DWang XZhu H(2020)Semi-quantum-honest key agreement scheme with three-particle entangled states in cross-realm settingQuantum Information Processing10.1007/s11128-020-02879-z19:10Online publication date: 8-Oct-2020
https://doi.org/10.1007/s11128-020-02879-z
Prousalis KKonofaos N(2019)Α Quantum Pattern Recognition Method for Improving Pairwise Sequence AlignmentScientific Reports10.1038/s41598-019-43697-39:1Online publication date: 10-May-2019
https://doi.org/10.1038/s41598-019-43697-3

View Options

Login options

Check if you have access through your login credentials or your institution to get full access on this article.

Cited By

Index Terms

Recommendations

Quantum algorithm for multiple alignment of amino acid sequences

Photonic scheme of quantum phase estimation for quantum algorithms via quantum dots

Quantum algorithm for preparing the ground state of a physical system through multi-step quantum resonant transitions

Comments

Published In

In-Cooperation

Publisher

Publication History

Permissions

Check for updates

Author Tags

Qualifiers

Conference

Other Metrics

Article Metrics

Other Metrics

Cited By

Login options

Full Access

PDF

eReader

Abstract

References

Cited By

Index Terms

Recommendations

Quantum algorithm for multiple alignment of amino acid sequences

Photonic scheme of quantum phase estimation for quantum algorithms via quantum dots

Quantum algorithm for preparing the ground state of a physical system through multi-step quantum resonant transitions

Comments

Information

Published In

In-Cooperation

Publisher

Publication History

Permissions

Check for updates

Author Tags

Qualifiers

Conference

Contributors

Other Metrics

Bibliometrics

Article Metrics

Other Metrics

Citations

Cited By

Login options

Full Access

View options

PDF

eReader

Figures

Other

Share

Share this Publication link

Share on social media

Affiliations