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.
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, -
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. 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