Skip to main content
SpringerLink
Log in

Partitional Clustering of Protein Sequences – An Inductive Logic Programming Approach

  • Conference paper
Distributed Computing, Artificial Intelligence, Bioinformatics, Soft Computing, and Ambient Assisted Living (IWANN 2009)

Part of the book series: Lecture Notes in Computer Science ((LNTCS,volume 5518))

Included in the following conference series:

  • 2651 Accesses

Abstract

We present a novel approach to cluster sets of protein sequences, based on Inductive Logic Programming (ILP). Preliminary results show that the method proposed produces understandable descriptions/explanations of the clusters. Furthermore, it can be used as a knowledge elicitation tool to explain clusters proposed by other clustering approaches, such as standard phylogenetic programs.

This work has been partially supported by the project ILP-Web-Service (PTDC/EIA/70841/2006) and by Fundação para a Ciência e Tecnologia. Nuno A. Fonseca is funded by FCT grant SFRH/BPD/26737/2006.

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

Access this chapter

Log in via an institution
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. Zelezný, F., Lavrač, N.: Propositionalization-based relational subgroup discovery with rsd. Machine Learning 62(1-2), 33–63 (2006)

    Article  Google Scholar 

  2. Fonseca, N.A., Camacho, R., Rocha, R., Costa, V.S.: Compile the hypothesis space: do it once, use it often. Fundamenta Informaticae, Special Issue on Multi-Relational Data Mining (89), 45–67 (2008)

    MATH  Google Scholar 

  3. Ralaivola, L., Swamidass, S.J., Saigo, H., Baldi, P.: Graph kernels for chemical informatics. Neural Netw. 18(8), 1093–1110 (2005)

    Article  Google Scholar 

  4. Hand, D.J., Smyth, P., Mannila, H.: Principles of data mining. MIT Press, Cambridge (2001)

    Google Scholar 

  5. Rice, P., Longden, I., Bleasby, A.: EMBOSS: The European Molecular Biology Open Software Suite. Trends in Genetics 6(16), 276–277 (2000)

    Article  Google Scholar 

  6. Pereira, P., Fonseca, N.A., Silva, F.: Fast Discovery of Statistically Interesting Words. Technical Report DCC-2007-01, DCC-FC & LIACC, Universidade do Porto (2007)

    Google Scholar 

  7. Conesa, A., Götz, S., García-Gómez, J.M., Terol, J., Talón, M., Robles, M.: Blast2GO: a universal tool for annotation, visualization and analysis in functional genomics research. Bioinformatics 21(18), 3674–3676 (2005)

    Article  Google Scholar 

  8. Ronquist, F., Huelsenbeck, J.P.: Mrbayes 3: Bayesian phylogenetic inference under mixed models. Bioinformatics 19(12), 1572–1574 (2003)

    Article  Google Scholar 

  9. Notredame, C., Higgins, D.G., Heringa, J.: T-coffee: A novel method for fast and accurate multiple sequence alignment. J. Mol. Biol. 302(1), 205–217 (2000)

    Article  Google Scholar 

Download references

Author information

Authors and Affiliations

  1. Instituto de Biologia Molecular e Celular (IBMC), Universidade do Porto, Rua do Campo Alegre 823, 4150-180, Porto, Portugal

    Nuno A. Fonseca, Cristina Vieira & Jorge Vieira

  2. CRACS-INESC Porto LA, Universidade do Porto, Rua do Campo Alegre 1021/1055, 4169-007, Porto, Portugal

    Nuno A. Fonseca & Vitor Santos Costa

  3. LIAAD-INESC Porto LA & FEUP, Universidade do Porto, Rua Dr Roberto Frias s/n, 4200-465, Porto, Portugal

    Rui Camacho

Authors
  1. Nuno A. Fonseca
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Vitor Santos Costa
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Rui Camacho
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Cristina Vieira
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Jorge Vieira
    View author publications

    You can also search for this author in PubMed Google Scholar

Editor information

Editors and Affiliations

  1. Graduate School of Engineering, Osaka Prefecture University, Osaka, Japan

    Sigeru Omatu

  2. Department of Informatics / CCTC, University of Minho, Braga, Portugal

    Miguel P. Rocha

  3. MAmI Research Lab, University of Castilla-La Mancha,, Ciudad Real, Spain

    José Bravo

  4. Department of Informatics, University of Vigo, Ourense, Spain

    Florentino Fernández

  5. Grupo de Investigación GICAP, Área de Lenguajes Higher Polytechnic School, Universidad de Burgos, Burgos, Spain

    Emilio Corchado

  6. Higher Polytechnic School, University of Burgos, Burgos, Spain

    Andrés Bustillo

  7. Department of Informatics, University of Salamanca, Salamanca, Spain

    Juan M. Corchado

Rights and permissions

Reprints and permissions

Copyright information

© 2009 Springer-Verlag Berlin Heidelberg

About this paper

Cite this paper

Fonseca, N.A., Costa, V.S., Camacho, R., Vieira, C., Vieira, J. (2009). Partitional Clustering of Protein Sequences – An Inductive Logic Programming Approach. In: Omatu, S., et al. Distributed Computing, Artificial Intelligence, Bioinformatics, Soft Computing, and Ambient Assisted Living. IWANN 2009. Lecture Notes in Computer Science, vol 5518. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-02481-8_152

Download citation

  • DOI: https://doi.org/10.1007/978-3-642-02481-8_152

  • Publisher Name: Springer, Berlin, Heidelberg

  • Print ISBN: 978-3-642-02480-1

  • Online ISBN: 978-3-642-02481-8

  • eBook Packages: Computer ScienceComputer Science (R0)

Publish with us

Policies and ethics

Search

Navigation