Research

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PhD

• Title:
  "DNA sequence filtration for finding long multiple approximate repetitions"
• Obtained the September 21, 2006. The jury was:
  • Marie-France Sagot (supervisor)
  • Maxime Crochemore (supervisor)
  • Gregory Kucherov (reviewer)
  • Christian Gautier (reviewer)
  • Jean Berstel (jury chairman)
  • Nadia Pisanti (invited)
  • Thierry Lecroq (invited)
  • Unfortunately, Mathieu Blanchette, reviewer, was not present
• Manuscript (4 MB - french)
• Slides (4.2 MB - french)

Main Research Topics

• Create Filters (essentially for DNA sequences) in order to speed up the multiple local alignment for finding long approximate multiple repetitions.
  • Leads to the creation of specific data structures like the bi-factor tree, the bi-factor array, ...
• How to take into account (very) large biological databases for BLAST-like programs?
  • Design and application of seeds for speeding up BLAST-like algorithm. Application on ReMIX, a reconfigurable architecture.
    Here is a general public presentation of the machine - (in french).
  • Investigation on word characteristics for reducing indexes sizes while inferring repetitions.

Available Tool

• Ed'Nimbus, a tool for filtering DNA sequences.

Publications

• International Journal Papers

  • P. Peterlongo, G. Sacamoto, A. Pereira do Lago, N. Pisanti, M.-F. Sagot
    Lossless enhanced filter for multiple similarity search
    In submission to BMC Algorithms for Molecular Biology
  • P. Peterlongo, L. Noé, D. Lavenier, J. Jacques, G. Kucherov, M. Giraud
    Efficient neighborhood storage for protein similarity search
    In submission to BMC Bioinformatics
  • P. Antoniou, M. Crochemore, C. S. Iliopoulos, P. Peterlongo
    Acquisition of common motifs with gaps in a set of sequences using sux trees
    In submission to Journal of Computational Biology
  • P. Peterlongo, N. Pisanti, F. Boyer, A. Pereira do Lago, M.-F. Sagot,
    Lossless filter for multiple repetitions with Hamming distance,
    Journal of Discrete Algorithms, -
  - DOI : 10.1016/j.jda.2007.03.003
  • P.Peterlongo, J. Allali, M-F.Sagot:
    Indexing gapped-factors using a tree,
    International Journal of Foundation of Computer Science, link -
  • C.S.Iliopoulos, J.McHugh, P.Peterlongo, N.Pisanti, W.Rytter, M.Sagot:
    A first approach to finding common motifs with gaps,
    International Journal of Foundation of Computer Science, 16(6), 1145--1155, 2005. -

• Conferences

  • P. Peterlongo, M. Gallé, F. Coste
    In place update of sux array while recoding words
    In preparation
  • P. Peterlongo, L. Noé, D. Lavenier, G. Georges, J. Jacques, G. Kucherov, M. Giraud
    Protein similarity search with subset seeds on a dedicated reconfigurable hardware,
    Proceedings of Parallel Bio-Computing (PBC 2007) - To appear in Springer LNCS
  • P. Antoniou, M. Crochemore, C.S. Iliopoulos, P. Peterlongo,
    Application of suffix trees for the acquisition of common motifs with gaps in a set of strings,
    Proceedings of International Conference on Language and Automata Theory and Applications (LATA 2007) -
  • P. Peterlongo, J. Allali, M.-F. Sagot,
    The Gapped-Factor Tree,
    Prague Stringology Conference (PSC 2006)
  • P. Antoniou, J. Holub, C.S. Iliopoulos, B. Melichar, P. Peterlongo,
    Finding Common Motifs with Gaps using Finite Automata,
    Proceedings of the 11th International Conference on Implementation and Application of Automata (CIAA 2006) -
  • P. Peterlongo, N. Pisanti, F. Boyer, M.-F. Sagot:
    Lossless Filter for Finding Long Multiple Approximate Repetitions Using a New Data Structure, the Bi-Factor Array,
    Proceedings of String Processing and Information Retrieval (SPIRE), Springer LNCS 3772, pages 179-190, 2005. -
  • C. Iliopoulos, J. McHugh, P. Peterlongo, N. Pisanti, W. Rytter, M.-F. Sagot:
    A First Approach to Finding Common Motifs with Gaps,
    Proceedings of Prague Stringology Conference (PSC), pages 88-97, 2004. -

• Poster

  • P. Peterlongo, N. Pisanti, A. Pereira do Lago, M.-F. Sagot,
    Ed'Nimbus: A Lossless Filter for Long Multiple Repetitions with Edit Distance ,
    Jobim 2006 - png (900 K, french)

• Technical report

  • P. Peterlongo, N. Pisanti, A. Pereira do Lago, M.-F. Sagot
    Lossless Filter for Long Multiple Repetitions with Edit Distance - ps.gz

Boabab

• Member of the Baobab team (Lyon)

Cooperations

• December 2006: Exchange with the University of Sao Paulo and the University of Campo Grande, Brazil. Work with Alair Pereira do Lago.
• September 2005: Exchange with the University of Sao Paulo, Brazil, work with Alair Pereira do Lago.
• October 2004: Cooperation with Jan Holub, Czech Technical University, Prague.
• April 2004: Cooperation with Costas S. Iliopoulos King's College London.