Skip to main content

Abstract

Advances in bioinformatics have contributed towards a significant increase in available information. Information analysis requires the use of distributed computing systems to best engage the process of data analysis. This study proposes a multiagent system that incorporates grid technology to facilitate distributed data analysis by dynamically incorporating the roles associated to each specific case study. The system was applied to genetic sequencing data to extract relevant information about insertions, deletions or polymorphisms.

This is a preview of subscription content, log in via an institution to check access.

Access this chapter

Chapter
USD 29.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 129.00
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 169.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Institutional subscriptions

Preview

Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.

References

  1. Mitchelson, K.R., Hawkes, D.B., Turakulov, R., Men, A.E.: Chapter Overview: Developments in DNA Sequencing. Perspectives in Bioanalysis 2, 3–44 (2007)

    Google Scholar 

  2. Soo, R.A., Wang, L.Z., Ng, S.S., Chong, P.Y., Yong, W.P., Lee, S.C., Liu, J.J., Choo, T.B., Tham, L.S., Lee, H.S., Goh, B.C., Soong, R.: Distribution of gemcitabine pathway genotypes in ethnic Asians and their association with outcome in non-small cell lung cancer patients. Lung Cancer 63(1), 121–127 (2009)

    Article  Google Scholar 

  3. Esteban, F., Royo, J.L., González-Moles, M.A., Gonzalez-Perez, A., Redondo, M., Moreno-Luna, R., Rodríguez-Sola, M., Gonzalez, A., Real, L.M., Ruiz, A., Ramírez-Lorca, R.: CAPN10 alleles modify laryngeal cancer risk in the Spanish population. European Journal of Surgical Oncology (EJSO) 34(1), 94–99 (2008)

    Article  Google Scholar 

  4. Zhang, J., Chiodini, R., Badr, A., Zhang, G.: The impact of next-generation sequencing on genomics. Journal of Genetics and Genomics 38(3), 95–109 (2011)

    Article  Google Scholar 

  5. Corchado, J.M., De Paz, J.F., Rodríguez, S., Bajo, J.: Model of experts for decision support in the diagnosis of leukemia patients. Artificial Intelligence in Medicine 46(3), 179–200 (2009)

    Article  Google Scholar 

  6. Gregoretti, F., Laccetti, G., Murlib, A., Olivaa, G., Scafuri, U.: MGF: A grid-enabled MPI library. Future Generation Computer Systems 24(2), 158–165 (2008)

    Article  Google Scholar 

  7. Jin, H., Jespersen, D., Mehrotra, P., Biswas, R., Huang, L., Chapman, B.: High performance computing using MPI and OpenMP on multi-core parallel systems. Parallel Computing (in Press)

    Google Scholar 

  8. Rakić, P.S., Milašinović, D.D., Živanov, Ž., Suvajdžin, Z., Nikolić, M., Hajduković, M.: MPI–CUDA parallelization of a finite-strip program for geometric nonlinear analysis: A hybrid approac. Advances in Engineering Software, 42(5), 273–285 (2011)

    Google Scholar 

  9. Wooldridge, M.: Introduction to Mult iAgent Systems. John Wiley & Sons (2002)

    Google Scholar 

  10. International Human Genome Sequencing Consortium, Finishing the euchromatic sequence of the human genome. Nature 431, 931–945 (2004)

    Google Scholar 

  11. Sahua, S.S., Pand, G.: dentification of Protein-Coding Regions DNA Sequences Using A Time-Frequency Filtering Approach. Genomics, Proteomics & Bioinformatics 9(1-2), 45–55 (2011)

    Article  Google Scholar 

  12. Khajeh-Saeed, A., Poole, S., Perot, J.B.: Acceleration of the Smith–Waterman algorithm using single and multiple graphics processors. Journal of Computational Physics 229(11), 4247–4258 (2010)

    Article  MathSciNet  MATH  Google Scholar 

  13. Altschul, S.F., Gish, W., Miller, W., Myers, E.W., Lipman, D.J.: Basic local alignment search tool. Journal of Molecular Biology 215(3), 403–410 (1990)

    Google Scholar 

  14. Kent, W.J.: BLAT—the BLAST-like alignment tool. Genome. Res. 12, 656–664 (2002)

    MathSciNet  Google Scholar 

  15. Margulies, M., Egholm, M., Altman, W.E., Attiya, S., Bader, J.S., Bemben, L.A., Berka, J., Braverman, M.S., Chen, Y.J., Chen, Z., Dewell, S.B., Du, L., Fierro, J.M., Gomes, X.V., Godwin, B.C., He, W., Helgesen, S., Ho, C.H., Irzyk, G.P., Jando, S.C., Alenquer, M.L., Jarvie, T.P., Jirage, K.B., Kim, J.B., Knight, J.R., Lanza, J.R., Leamon, J.H., Lefkowitz, S.M., Lei, M., Li, J., Lohman, K.L., Lu, H., Makhijani, V.B., McDade, K.E., McKenna, M.P., Myers, E.W., Nickerson, E., Nobile, J.R., Plant, R., Puc, B.P., Ronan, M.T., Roth, G.T., Sarkis, G.J., Simons, J.F., Simpson, J.W., Srinivasan, M., Tartaro, K.R., Tomasz, A., Vogt, K.A., Volkmer, G.A., Wang, S.H., Wang, Y., Weiner, M.P., Yu, P., Begley, R.F., Rothberg, J.M.: Genome sequencing in microfabricated high-density picolitre reactors. Nature 437, 376–380 (2005)

    Google Scholar 

  16. Miller, J.R., Koren, S., Sutton, G.: Assembly algorithms for next-generation sequencing data. Genomics 95(6), 315–327 (2010)

    Article  Google Scholar 

Download references

Author information

Authors and Affiliations

Authors

Corresponding author

Correspondence to Roberto González .

Editor information

Editors and Affiliations

Rights and permissions

Reprints and permissions

Copyright information

© 2012 Springer-Verlag Berlin Heidelberg

About this paper

Cite this paper

González, R., Zato, C., Benito, R., Hernández, M., Hernández, J.M., De Paz, J.F. (2012). SAMasGC: Sequencing Analysis with a Multiagent System and Grid Computing. In: Rocha, M., Luscombe, N., Fdez-Riverola, F., Rodríguez, J. (eds) 6th International Conference on Practical Applications of Computational Biology & Bioinformatics. Advances in Intelligent and Soft Computing, vol 154. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-28839-5_24

Download citation

  • DOI: https://doi.org/10.1007/978-3-642-28839-5_24

  • Publisher Name: Springer, Berlin, Heidelberg

  • Print ISBN: 978-3-642-28838-8

  • Online ISBN: 978-3-642-28839-5

  • eBook Packages: EngineeringEngineering (R0)

Publish with us

Policies and ethics