Protein Similarity Search with Subset Seeds on a Dedicated Reconfigurable Hardware (2009)
Pierre Peterlongo, Dominique Lavenier, Gilles Georges, Julien Jacques, Gregory Kucherov, Mathieu Giraud
Abstract. With a sharp increase of available DNA and protein sequence data, new precise and fast similarity search methods are needed for largescale genome and proteome comparisons. Modern seed-based...
Lossless filter for multiple repeats with bounded edit distance (2009)
Peterlongo, Pierre, Sacomoto, Gustavo, Do Lago, Alair, Pisanti, Nadia, Sagot, Marie-France
Abstract Background Identifying local similarity between two or more sequences, or identifying repeats occurring at least twice in a sequence, is an essential part in the analysis of biological...
c-GAMMA: Comparative Genome Analysis of Molecular Markers (2009)
Peterlongo, Pierre, Nicolas, Jacques, Lavenier, Dominique, Vorc'H, Raoul, Querellou, Joël
Discovery of molecular markers for efficient identification of living organisms remains a challenge of high interest. The diversity of species can now be observed in details with low cost genomic...
Lossless filter for multiple repeats with bounded edit distance. (2009)
Peterlongo, Pierre, Sacomoto, Gustavo Akio Tominaga, Do Lago, Alair Pereira, Pisanti, Nadia, Sagot, Marie-France
BACKGROUND: Identifying local similarity between two or more sequences, or identifying repeats occurring at least twice in a sequence, is an essential part in the analysis of biological sequences and...
c-GAMMA: Comparative Genome Analysis of Molecular Markers (2009)
Peterlongo, Pierre, Nicolas, Jacques, Lavenier, Dominique, Vorc'H, Raoul, Querellou, Joël
Discovery of molecular markers for efficient identification of living organisms remains a challenge of high interest. The diversity of species can now be observed in details with low cost genomic...
Lossless filter for multiple repeats with bounded edit distance. (2009)
Peterlongo, Pierre, Sacomoto, Gustavo Akio Tominaga, Do Lago, Alair Pereira, Pisanti, Nadia, Sagot, Marie-France
BACKGROUND: Identifying local similarity between two or more sequences, or identifying repeats occurring at least twice in a sequence, is an essential part in the analysis of biological sequences and...
Optimal neighborhood indexing for protein similarity search (2008)
Peterlongo, Pierre, Noé, Laurent, Lavenier, Dominique, Nguyen, Van, Kucherov, Gregory, Giraud, Mathieu
Abstract Background Similarity inference, one of the main bioinformatics tasks, has to face an exponential growth of the biological data. A classical approach used to cope with this data flow...
Pierre Peterlongo, Laurent Noé, Dominique Lavenier, Gilles Georges, Julien Jacques, Gregory Kucherov, ...
similarity search with subset seeds
Pierre Peterlongo, Julien Allali, Marie-france Sagot
Communicated by Editor’s name We present a data structure to index a specific kind of factors, that is of substrings, called gapped-factors. A gapped-factor is a factor containing a gap that is...
Pierre Peterlongo, Julien Allali, Marie-france Sagot
Communicated by Editor’s name We present a data structure to index a specific kind of factors, that is of substrings, called gapped-factors. A gapped-factor is a factor containing a gap that is...
Finding Common Motifs with Gaps using Finite Automata ⋆ (2008)
Pavlos Antoniou, Jan Holub, Costas S. Iliopoulos, Pierre Peterlongo
Abstract. We present an algorithm that uses finite automata to find the common motifs with gaps occurring in all strings belonging to a finite set S = {S1, S2,..., Sr}. In order to find these common...
motifs with gaps in a set (2008)
Pavlos Antoniou, Maxime Crochemore, Costas S. Iliopoulos, Pierre Peterlongo
Application of suffix trees for the acquisition of common
In-place Update of Suffix Array while Recoding Words (2008)
Gallé, Matthias, Peterlongo, Pierre, Coste, François
Motivated by grammatical inference and data compression applications, we propose an algorithm to update a suffix array after the substitution, in the indexed text, of some occurrences of a given word...
In-place Update of Suffix Array while Recoding Words (2008)
Gallé, Matthias, Peterlongo, Pierre, Coste, François
Motivated by grammatical inference and data compression applications, we propose an algorithm to update a suffix array after the substitution, in the indexed text, of some occurrences of a given word...
Optimal neighborhood indexing for protein similarity search (2008)
Peterlongo, Pierre, Noé, Laurent, Lavenier, Dominique, Nguyen, Van Hoa, Kucherov, Gregory, Giraud, Mathieu
Similarity inference, one of the main bioinformatics tasks, has to face an exponential growth of the biological data. A classical approach used to cope with this data flow involves heuristics with...
Optimal neighborhood indexing for protein similarity search (2008)
Peterlongo, Pierre, Noé, Laurent, Lavenier, Dominique, Nguyen, Van Hoa, Kucherov, Gregory, Giraud, Mathieu
Similarity inference, one of the main bioinformatics tasks, has to face an exponential growth of the biological data. A classical approach used to cope with this data flow involves heuristics with...
Modeling local repeats on genomic sequences (2008)
Nicolas, Jacques, Rousseau, Christine, Siegel, Anne, Peterlongo, Pierre, Coste, François, Durand, Patrick, ...
This paper deals with the specification and search of repeats of biological interest, i.e. repeats that may have a role in genomic structures or functions. Although some particular repeats such as...
Modeling local repeats on genomic sequences (2008)
Nicolas, Jacques, Rousseau, Christine, Siegel, Anne, Peterlongo, Pierre, Coste, François, Durand, Patrick, ...
This paper deals with the specification and search of repeats of biological interest, i.e. repeats that may have a role in genomic structures or functions. Although some particular repeats such as...
Protein similarity search with subset seeds on a dedicated reconfigurable hardware (2008)
Pierre Peterlongo, Laurent Noé, Dominique Lavenier, Gilles Georges, Julien Jacques, Gregory Kucherov, ...
Genome sequencing of numerous species raises the need of complete genome comparison with precise and fast similarity searches. Today, advanced seed-based techniques (spaced seeds, multiple seeds,...
Optimal neighborhood indexing for protein similarity search (2008)
Pierre Peterlongo, Laurent Noé, Dominique Lavenier, Van Hoa Nguyen, Gregory Kucherov, Mathieu Giraud
Background Similarity inference, one of the main bioinformatics tasks, has to face an exponential growth of the biological data. A classical approach used to cope with this data flow involves...
Filtrage de séquences d'ADN pour la recherche de longues répétitions multiples (2007)
La génomique moléculaire fait face en ce début de siècle à de nouvelles situations qu'elle doit prendre en compte. D'une part, depuis une dizaine d'années, la quantité de données disponibles...
Protein similarity search with subset seeds on a dedicated reconfigurable hardware (2007)
Peterlongo, Pierre, Noé, Laurent, Lavenier, Dominique, Georges, Gilles, Jacques, Julien, Kucherov, Gregory, ...
Genome sequencing of numerous species raises the need of complete genome comparison with precise and fast similarity searches. Today, advanced seed-based techniques (spaced seeds, multiple seeds,...
Protein similarity search with subset seeds on a dedicated reconfigurable hardware (2007)
Peterlongo, Pierre, Noé, Laurent, Lavenier, Dominique, Georges, Gilles, Jacques, Julien, Kucherov, Gregory, ...
Genome sequencing of numerous species raises the need of complete genome comparison with precise and fast similarity searches. Today, advanced seed-based techniques (spaced seeds, multiple seeds,...
Lossless filter for multiple repetitions with Hamming distance (2007)
Peterlongo, Pierre, Pisanti, Nadia, Boyer, Frédéric, Pereira Do Lago, Alair, Sagot, Marie-France
Similarity search in texts, notably in biological sequences, has received substantial attention in the last few years. Numerous filtration and indexing techniques have been created in order to...
Lossless filter for multiple repetitions with Hamming distance (2007)
Peterlongo, Pierre, Pisanti, Nadia, Boyer, Frédéric, Pereira Do Lago, Alair, Sagot, Marie-France
Similarity search in texts, notably in biological sequences, has received substantial attention in the last few years. Numerous filtration and indexing techniques have been created in order to...
Indexing gapped-factors using a tree (2007)
Peterlongo, Pierre, Allali, Julien, Sagot, Marie-France
We present a data structure to index a specific kind of factors, that is of substrings, called gapped-factors. A gapped-factor is a factor containing a gap that is ignored during the...
Indexing gapped-factors using a tree (2007)
Peterlongo, Pierre, Allali, Julien, Sagot, Marie-France
We present a data structure to index a specific kind of factors, that is of substrings, called gapped-factors. A gapped-factor is a factor containing a gap that is ignored during the...
Antoniou, Pavlos, Crochemore, Maxime, Iliopoulos, Costas, Peterlongo, Pierre
The inference of common motifs in a set of strings is a well-known problem with many applications in biological sciences. We study a new variant of this problem that oers a solution with the added...
Antoniou, Pavlos, Crochemore, Maxime, Iliopoulos, Costas, Peterlongo, Pierre
The inference of common motifs in a set of strings is a well-known problem with many applications in biological sciences. We study a new variant of this problem that oers a solution with the added...
Filtrage de séquences d'ADN pour la recherche de longues répétitions multiples (2006)
La génomique moléculaire fait face en ce début de siècle à de nouvelles situations qu'elle doit prendre en compte. D'une part, depuis une dizaine d'années, la quantité de données disponibles...
Filtrage de séquences d'ADN pour la recherche de longues répétitions multiples (2006)
La génomique moléculaire fait face en ce début de siècle à de nouvelles situations qu'elle doit prendre en compte. D'une part, depuis une dizaine d'années, la quantité de données disponibles...
Filtrage de séquences d'ADN pour la recherche de longues répétitions multiples (2006)
La génomique moléculaire fait face en ce début de siècle à de nouvelles situations qu'elle doit prendre en compte. D'une part, depuis une dizaine d'années, la quantité de données disponibles...
Peterlongo, Pierre, Allali, Julien, Sagot, Marie-France
We present a data structure to index a specific kind of factors, that is of substrings, called gapped-factors. A gapped-factor is a factor containing a gap that is ignored during the indexation. The...
Peterlongo, Pierre, Allali, Julien, Sagot, Marie-France
We present a data structure to index a specific kind of factors, that is of substrings, called gapped-factors. A gapped-factor is a factor containing a gap that is ignored during the indexation. The...
Pierre Peterlongo, Nadia Pisanti, Frederic Boyer
Abstract. Similarity search in texts, notably biological sequences, has received substantial attention in the last few years. Numerous filtration and indexing techniques have been created in order to...