Skip to main content
Disciplines
Automotive Business IT + Informatics Construction + Real Estate Electrical Engineering + Electronics Energy + Sustainability Insurance + Risk Finance + Banking Management + Leadership Marketing + Sales Mechanical Engineering + Materials
Events
DE
EN
Books
Journals
Topic Page
Marketing
Start single access now
Access for companies
EXTENDED SEARCH
Log in
Top
Published in:
Quality Assessment and Classification of Heart Sounds Using PCG Signals Read chapter Read first chapter

2019 | OriginalPaper | Chapter

Parallel Computation on Large-Scale DNA Sequences

Authors : Abdul Majid, Mukhtaj Khan, Mushtaq Khan, Jamil Ahmad, Maozhen Li, Rehan Zafar Paracha

Published in: Applications of Intelligent Technologies in Healthcare

Publisher: Springer International Publishing

Log in

Activate our intelligent search to find suitable subject content or patents.

search-config
loading …

Abstract

With the advent of next-generation DNA sequencing technology, the field of bioinformatics and computational biology is becoming increasingly complex and computationally intensive. The bioinformatics community faces the challenge of finding suitable methods to solve growing computational issues, for instance, processing of massive volumes of DNA sequences. Such method can be found in the field of high-performance computing through parallel processing. In this paper we have proposed parallel approach which is built on top of modified VSM. The proposed method is parallelized computation on a number of available processing cores in order to minimize computation time and support analysis of a large number of DNA sequences analysis.

Dont have a licence yet? Then find out more about our products and how to get one now:

Springer Professional "Wirtschaft+Technik"

Online-Abonnement

Mit Springer Professional "Wirtschaft+Technik" erhalten Sie Zugriff auf:

  • über 102.000 Bücher
  • über 537 Zeitschriften

aus folgenden Fachgebieten:

  • Automobil + Motoren
  • Bauwesen + Immobilien
  • Business IT + Informatik
  • Elektrotechnik + Elektronik
  • Energie + Nachhaltigkeit
  • Finance + Banking
  • Management + Führung
  • Marketing + Vertrieb
  • Maschinenbau + Werkstoffe
  • Versicherung + Risiko

Jetzt Wissensvorsprung sichern!

inform now

Springer Professional "Technik"

Online-Abonnement

Mit Springer Professional "Technik" erhalten Sie Zugriff auf:

  • über 67.000 Bücher
  • über 390 Zeitschriften

aus folgenden Fachgebieten:

  • Automobil + Motoren
  • Bauwesen + Immobilien
  • Business IT + Informatik
  • Elektrotechnik + Elektronik
  • Energie + Nachhaltigkeit
  • Maschinenbau + Werkstoffe




 

Jetzt Wissensvorsprung sichern!

inform now

Springer Professional "Wirtschaft"

Online-Abonnement

Mit Springer Professional "Wirtschaft" erhalten Sie Zugriff auf:

  • über 67.000 Bücher
  • über 340 Zeitschriften

aus folgenden Fachgebieten:

  • Bauwesen + Immobilien
  • Business IT + Informatik
  • Finance + Banking
  • Management + Führung
  • Marketing + Vertrieb
  • Versicherung + Risiko




Jetzt Wissensvorsprung sichern!

inform now
previous chapter A Privacy Risk Assessment for the Internet of Things in Healthcare
next chapter Augmented and Virtual Reality in Mobile Fitness Applications: A Survey
Literature
1.
Bald, P., Baronio, R., Cristofaro, E. D., Gasti, P., & Tsudik, G. (2000). Efficient and secure testing of fully-sequenced human genomes. Biological Sciences Initiative, 470, 7–10.
2.
Memeti, S., & Pllana, S. 2016. Analyzing large-scale DNA sequences on multi-core architectures. Proceedings – IEEE 18th international conference on computational science and engineering CSE 2015, pp. 208–215.
3.
Ogheneovo, E. E., & Japheth, R. B. (2016). Application of vector space model to query ranking and information retrieval. International Journal of Advanced Research in Computer Science and Software Engineering, 6(5), 42–47.
4.
Smith, T. F., & Waterman, M. S. (1981). Identification of common molecular subsequences. Journal of Molecular Biology, 147(1), 195–197.CrossRef
5.
Dereeper, A., Audic, S., Claverie, J.-M., & Blanc, G. (2010). BLAST-EXPLORER helps you building datasets for phylogenetic analysis. BMC Evolutionary Biology, 10(1), 8.CrossRef
6.
Abual-Rub, M., Abdullah, R., & Rashid, N. (2007). A modified vector space model for protein retrieval. International Journal of Computer Science and Network Security, 7(9), 85–89.
7.
Patel, S., Panchal, H., & Anjaria, K. (2012). DNA sequence analysis by ORF FINDER amp; GENOMATIX tool: Bioinformatics analysis of some tree species of Leguminosae family, in 2012 IEEE international conference on bioinformatics and biomedicine workshops, pp. 922–926.
8.
Vandin, F., Upfal, E., & Raphael, B. J. (2012, March). Algorithms and Genome Sequencing : Identifying Driver Pathways in Cancer. IEEE Computer Magazine, 45(3), 39–46.CrossRef
9.
Benson, D. A., Cavanaugh, M., Clark, K., Karsch-mizrachi, I., Lipman, D. J., Ostell, J., & Sayers, E. W. (2013). GenBank. Nucleic Acids Research, 41(D1 November 2012), 36–42.CrossRef
10.
de Almeida, T. J. B. M., & Roma, N. F. V. (2010, February). A Parallel Programming Framework for Multi-core DNA Sequence Alignment, 2010 international conference on Complex, Intelligent and Software Intensive Systems (CISIS), 2010, pp. 907–912.
11.
Marçais, G., & Kingsford, C. (2011). A fast, lock-free approach for efficient parallel counting of occurrences of k-mers. Bioinformatics, 27(6), 764–770.CrossRef
12.
Herath, D., Lakmali, C., Ragel, R. (2012, March). Accelerating string matching for bio-computing applications on multi-core CPUs. IEEE 7th, Int. Conf. Ind. Inf. Syst. ICIIS 2012.
13.
Takeuchi, T., Yamada, A., Aoki, T., & Nishimura, K. (2016). cljam: A library for handling DNA sequence alignment/map (SAM) with parallel processing. Source Code for Biology and Medicine, 11, 1–4.CrossRef
14.
Manning, C. D., Raghavan, P., & Schütze, H. (2008), An introduction to information retrieval, Cambridge University Press, 2008.
15.
Raghavan, V. V., & Wong, S. K. M. (1986). A critical analysis of vector space model for information retrieval. Journal of the American Society for Information Science, 37(5), 279--287.CrossRef
16.
Singhal, A. (2001). Modern information retrieval : A brief overview. IEEE Data Engineering Bulletin, 24, 35–43.
17.
Castells, P., Fernandez, M., & Vallet, D. (Feb. 2007). An adaptation of the vector-space model for ontology-based information retrieval. IEEE Transactions on Knowledge and Data Engineering, 19(2), 261–272.CrossRef
18.
Sarkar, I. N. (2012). A vector space model approach to identify genetically related diseases. Journal of the American Medical Informartion Association, 19(2), 249–254.CrossRef
19.
Metadata
Title
Parallel Computation on Large-Scale DNA Sequences
Authors
Abdul Majid
Mukhtaj Khan
Mushtaq Khan
Jamil Ahmad
Maozhen Li
Rehan Zafar Paracha
Copyright Year
2019
Book
Applications of Intelligent Technologies in Healthcare

Print ISBN: 978-3-319-96138-5

Electronic ISBN: 978-3-319-96139-2

Copyright Year: 2019

DOI
https://doi.org/10.1007/978-3-319-96139-2_6