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...
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
Sébastien Tempel, Mathieu Giraud, Dominique Lavenier, Israël-césar Lerman, Sophie Valin, Ivan Couée, ...
Motivation: The analysis of repeated elements in genomes is a fascinating domain of research that is lacking relevant tools for transposable elements, the most complex ones. The dynamics of...
Seed-Based Exclusion Method for Non-Coding RNA Gene Search (2008)
Jean-eudes Duchesne, Mathieu Giraud, Nadia El-mabrouk
Abstract. Given an RNA family characterized by conserved sequences and folding constraints, the problem is to search for all the instances of the RNA family in a genomic database. As seed-based...
application to the study of a family (2008)
Sébastien Tempel, Mathieu Giraud, Dominique Lavenier, Israël-césar Lerman, Anne-sophie Valin, Ivan Couée, ...
doi:10.1093/bioinformatics/btl337
Seed-Based Exclusion Method for Non-coding RNA Gene Search (2008)
Jean-eudes Duchesne, Mathieu Giraud, Nadia El-mabrouk
Abstract. Given an RNA family characterized by conserved sequences and folding constraints, the problem is to search for all the instances of the RNA family in a genomic database. As seed-based...
Mathieu Giraud, Phillipe Veber, Dominique Lavenier
Communicated by Editor’s name Weighted finite automata (WFA) are used with FPGA accelerating hardware to scan large genomic banks. Hardwiring such automata raises surface area and clock frequency...
Not so many runs in strings (2008)
Since the work of Kolpakov and Kucherov in 1998, it is known that \rho(n), the maximal number of runs in a string, is linear in the length n of the string. A lower bound of 3/(1 + \sqrt{5}) n = 0.927...
Not so many runs in strings (2008)
Since the work of Kolpakov and Kucherov in 1998, it is known that \rho(n), the maximal number of runs in a string, is linear in the length n of the string. A lower bound of 3/(1 + \sqrt{5}) n = 0.927...
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...
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...
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,...
Seed-Based Exclusion Method for Non-coding RNA Gene Search (2007)
Duchesne, Jean-Eudes, Giraud, Mathieu, El-Mabrouk, Nadia
Given an RNA family characterized by conserved sequences and folding constraints, the problem is to search for all the instances of the RNA family in a genomic database. As seed-based heuristics have...
Path-equivalent developments in acyclic weighted automata (2007)
Giraud, Mathieu, Veber, Philippe, Lavenier, Dominique
Weighted finite automata (WFA) are used with FPGA accelerating hardware to scan large genomic banks. Hardwiring such automata raises surface area and clock frequency constraints, requiring...
Seed-Based Exclusion Method for Non-coding RNA Gene Search (2007)
Duchesne, Jean-Eudes, Giraud, Mathieu, El-Mabrouk, Nadia
Given an RNA family characterized by conserved sequences and folding constraints, the problem is to search for all the instances of the RNA family in a genomic database. As seed-based heuristics have...
Path-equivalent developments in acyclic weighted automata (2007)
Giraud, Mathieu, Veber, Philippe, Lavenier, Dominique
Weighted finite automata (WFA) are used with FPGA accelerating hardware to scan large genomic banks. Hardwiring such automata raises surface area and clock frequency constraints, requiring...
Graines espacées et recherche d’ARN non-codants (2007)
Arnaud Fontaine, Mathieu Giraud, Laurent Noé
Sequence comparison is widely used to help discovering novel non-coding RNAs in newly sequenced genomes. In this context, Blast-like homology search tools are of great interest. We show here that the...
Path-Equivalent Removals of ε-transitions in a Genomic Weighted Finite Automaton (2006)
Mathieu Giraud, Philippe Veber, Dominique Lavenier
Weighted finite automata (WFA) are used with accelerating hardware to scan large genomic banks. Hardwiring such automata raise surface area and clock frequency constraints, requiring e#cient...
Team sequoia - Algorithms for large-scale sequence analysis - INRIA Activity Report (2006)
Gregory Kucherov, Hélène Touzet, Mathieu Giraud, Maude Pupin, Jean-Stéphane Varré, Laurent Noé, ...
Tempel, Sébastien, Giraud, Mathieu, Lavenier, Dominique, Lerman, Israël-César, Valin, Anne-Sophie, Couée, Ivan, ...
Motivation: The analysis of repeated elements in genomes is a fascinating domain of research that is lacking relevant tools for transposable elements (TEs), the most complex ones. The dynamics of...
Giraud, Mathieu, Noé, Laurent, Kucherov, Gregory, Lavenier, Dominique
Ce tutoriel expose certains problèmes fondamentaux en algorithmique du texte pour la bioinformatique, leurs solutions actuelles ainsi que quelques perspectives de recherche. Après une introduction...
Bioinformatics Applications (2005)
Lavenier, Dominique, Giraud, Mathieu
The rapid growth of biotechnologies, especially in large sequencing projects, has lead to an explosion of genomic data. For molecular biologists, this mass of data is potentially a rich source of...
Bioinformatics Applications (2005)
Lavenier, Dominique, Giraud, Mathieu
The rapid growth of biotechnologies, especially in large sequencing projects, has lead to an explosion of genomic data. For molecular biologists, this mass of data is potentially a rich source of...
The dog and rat olfactory receptor repertoires (2005)
Quignon, Pascale, Giraud, Mathieu, Rimbault, Maud, Lavigne, Patricia, Tacher, Sandrine, Morin, Emmanuelle, ...
Abstract Background Dogs and rats have a highly developed capability to detect and identify odorant molecules, even at minute concentrations. Previous analyses have shown that the olfactory receptors...
Tempel, Sébastien, Giraud, Mathieu, Lerman, Israel, Couée, Ivan, El-Amrani, Abdellak, Nicolas, Jacques
Giraud, Mathieu, Noé, Laurent, Kucherov, Gregory, Lavenier, Dominique
Ce tutoriel expose certains problèmes fondamentaux en algorithmique du texte pour la bioinformatique, leurs solutions actuelles ainsi que quelques perspectives de recherche. Après une introduction...
Giraud, Mathieu, Noé, Laurent, Kucherov, Gregory, Lavenier, Dominique
Ce tutoriel expose certains problèmes fondamentaux en algorithmique du texte pour la bioinformatique, leurs solutions actuelles ainsi que quelques perspectives de recherche. Après une introduction...
Linear Encoding Scheme for Weighted Finite Automata (2005)
Mathieu Giraud, Dominique Lavenier
In this paper, we show that the linear encoding scheme e#- ciently implements weighted finite automata (WFA). WFA with t transitions can be hardwired with O(t) cells. They solve pattern matching...
Dealing with Size Limits in a Hardware Encoding of Weighted Finite Automata (2004)
Mathieu Giraud, Dominique Lavenier
the maximum incoming degree. Prototype Implementation. Our practical implementation uses the R-disk prototype, a parallel architecture designed for mass data ltering [6]. Data is distributed among...
Maximal repetitions and Application to DNA sequences (2000)
Mathieu Giraud, Gregory Kucherov
In this paper we describe an implementation of Main-Kolpakov-Kucherov algorithm [9] of linear-time search for maximal repetitions in sequences. We first present a theoretical background and sketch...
Maximal tandem repetitions and Applications to DNA words (1999)
Mathieu Giraud, Loria Nancy, Directed Gregory Kucherov, Directed Gregory Kucherov
In this report, we explain our work on tandem repetitions. We implemented the Main-Kucherov-Kolpakov algorithm [KK98], and experimented it on real DNA chains. This algorithm finds all maximal tandem...
The dog and rat olfactory receptor repertoires
Quignon, Pascale, Giraud, Mathieu, Rimbault, Maud, Lavigne, Patricia, Tacher, Sandrine, Morin, Emmanuelle, ...
An almost complete list of odorant receptor genes in the dog (1,094 genes) and the rat (1,493 genes) is described. A comparison of odorant receptor repertoires in rat, dog, mouse and human is also...
The dog and rat olfactory receptor repertoires
Quignon, Pascale, Giraud, Mathieu, Rimbault, Maud, Lavigne, Patricia, Tacher, Sandrine, Morin, Emmanuelle, ...
An almost complete list of odorant receptor genes in the dog (1,094 genes) and the rat (1,493 genes) is described. A comparison of odorant receptor repertoires in rat, dog, mouse and human is also...