On subset seeds for protein alignment (2009)
Roytberg, Mikhail A., Gambin, Anna, Noé, Laurent, Lasota, Slawomir, Furletova, Eugenia, Szczurek, Ewa, ...
We apply the concept of subset seeds proposed in [1] to similarity search in protein sequences. The main question studied is the design of efficient seed alphabets to construct seeds with optimal...
Multiseed Lossless Filtration (2009)
Kucherov, Gregory, Noé, Laurent, Roytberg, Mikhail A.
We study a method of seed-based lossless filtration for approximate string matching and related bioinformatics applications. The method is based on a simultaneous use of several spaced seeds rather...
On subset seeds for protein alignment (2009)
Roytberg, Mikhail, Gambin, Anna, Noé, Laurent, Lasota, Slawomir, Furletova, Eugenia, Szczurek, Ewa, ...
We apply the concept of subset seeds proposed in [1] to similarity search in protein sequences. The main question studied is the design of efficient seed alphabets to construct seeds with optimal...
On subset seeds for protein alignment (2009)
Roytberg, Mikhail, Gambin, Anna, Noé, Laurent, Lasota, Slawomir, Furletova, Eugenia, Szczurek, Ewa, ...
We apply the concept of subset seeds proposed in [1] to similarity search in protein sequences. The main question studied is the design of efficient seed alphabets to construct seeds with optimal...
On subset seeds for protein alignment (2009)
Mikhail Roytberg, Anna Gambin, Laurent Noé, Slawomir Lasota, Eugenia Furletova, Ewa Szczurek, ...
We apply the concept of subset seeds proposed in [1] to similarity search in protein sequences. The main question studied is the design of efficient seed alphabets to construct seeds with optimal...
Improved Sensitivity And Reliability Of Anchor Based Genome Alignment (2009)
Uricaru, Raluca, Michotey, Célia, Noé, Laurent, Chiapello, Hélène, Rivals, Eric
Whole genome alignment is a challenging problem in computational comparative genomics. It is essential for the functional annotation of genomes, the understanding of their evolution, and for...
Improved Sensitivity And Reliability Of Anchor Based Genome Alignment (2009)
Uricaru, Raluca, Michotey, Célia, Noé, Laurent, Chiapello, Hélène, Rivals, Eric
Whole genome alignment is a challenging problem in computational comparative genomics. It is essential for the functional annotation of genomes, the understanding of their evolution, and for...
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
Efficient seeding techniques for protein similarity search (2008)
Roytberg, Mihkail, Gambin, Anna, Noé, Laurent, Lasota, Slawomir, Furletova, Eugenia, Szczurek, Ewa, ...
We apply the concept of subset seeds proposed in [1] to similarity search in protein sequences. The main question studied is the design of efficient seed alphabets to construct seeds with optimal...
de recherche YASS: Similarity search in DNA sequences (2008)
Laurent Noé, Gregory Kucherov, Laurent Noé, Gregory Kucherov, Thème Génie Logiciel, Projet Adage
apport
Multi-seed lossless filtration (Extended abstract) (2008)
Gregory Kucherov, Laurent Noé, Mikhail Roytberg
Abstract. We study a method of seed-based lossless filtration for approximate string matching and related applications. The method is based on a simultaneous use of several spaced seeds rather than a...
Efficient seeding techniques for protein similarity search (2008)
Roytberg, Mihkail, Gambin, Anna, Noé, Laurent, Lasota, Slawomir, Furletova, Eugenia, Szczurek, Ewa, ...
We apply the concept of subset seeds proposed in [1] to similarity search in protein sequences. The main question studied is the design of efficient seed alphabets to construct seeds with optimal...
Efficient seeding techniques for protein similarity search (2008)
Roytberg, Mihkail, Gambin, Anna, Noé, Laurent, Lasota, Slawomir, Furletova, Eugenia, Szczurek, Ewa, ...
We apply the concept of subset seeds proposed in [1] to similarity search in protein sequences. The main question studied is the design of efficient seed alphabets to construct seeds with optimal...
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...
Efficient seeding techniques for protein similarity search (2008)
Mikhail Roytberg, Anna Gambin, Laurent Noé, Slawomir Lasota, Eugenia Furletova, Ewa Szczurek, ...
We apply the concept of subset seeds proposed in [1] to similarity search in protein sequences. The main question studied is the design of efficient seed alphabets to construct seeds with optimal...
Protein sequence alignment via anti-translation (2008)
Marta Gîrdea, Gregory Kucherov, Laurent Noé
We propose a new approach to protein sequence alignment, where the basic idea is to find the best pairwise alignment between two DNA sequences, each of which encodes one of the given proteins. A...
Efficient seeding techniques for protein similarity search (2008)
Mikhail Roytberg, Anna Gambin, Laurent Noé, Slawomir Lasota, Eugenia Furletova, Ewa Szczurek, ...
We apply the concept of subset seeds proposed in [1] to similarity search in protein sequences. The main question studied is the design of efficient seed alphabets to construct seeds with optimal...
Kucherov, Gregory, Noé, Laurent, Roytberg, Mihkail
We study the pattern matching automaton introduced in [KucherovNoeRoytbergJBCB06] for the purpose of seed-based similarity search. We show that our definition provides a compact automaton, much...
Kucherov, Gregory, Noé, Laurent, Roytberg, Mihkail
We study the pattern matching automaton introduced in [KucherovNoeRoytbergJBCB06] for the purpose of seed-based similarity search. We show that our definition provides a compact automaton, much...
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,...
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...
Reconsidering the significance of genomic word frequencies (2007)
Miklós Csürös, Laurent Noé, Gregory Kucherov
By conventional wisdom, a feature that occurs too often or too rarely in a genome can indicate a functional element. To infer functionality from frequency, it is crucial to precisely characterize...
Gregory Kucherov, Laurent Noé, Mikhail Roytberg
We study the pattern matching automaton introduced in [1] for the purpose of seed-based similarity search. We show that our definition provides a compact automaton, much smaller than the one obtained...
Gregory Kucherov, Laurent Noé, Mikhail Roytberg
We study the pattern matching automaton introduced in [1] for the purpose of seed-based similarity search. We show that our definition provides a compact automaton, much smaller than the one obtained...
Reconsidering the significance of genomic word frequency (2006)
Csűrös, Miklós, Noé, Laurent, Kucherov, Gregory
We propose that the distribution of DNA words in genomic sequences can be primarily characterized by a double Pareto-lognormal distribution, which explains lognormal and power-law features found...
Les méthodes de recherche de similarités les plus fréquemment utilisées dans le cadre de la génomique sont heuristiques. Elles se basent sur un principe de filtrage du texte qui permet de...
Les méthodes de recherche de similarités les plus fréquemment utilisées dans le cadre de la génomique sont heuristiques. Elles se basent sur un principe de filtrage du texte qui permet de...
A unifying framework for seed sensitivity and its application to subset seeds (2006)
Kucherov, Gregory, Noé, Laurent, Roytberg, Mihkail
We propose a general approach to compute the seed sensitivity, that can be applied to different definitions of seeds. It treats separately three components of the seed sensitivity problem -- a set of...
Les méthodes de recherche de similarités les plus fréquemment utilisées dans le cadre de la génomique sont heuristiques. Elles se basent sur un principe de filtrage du texte qui permet de...
Les méthodes de recherche de similarités les plus fréquemment utilisées dans le cadre de la génomique sont heuristiques. Elles se basent sur un principe de filtrage du texte qui permet de...
A unifying framework for seed sensitivity and its application to subset seeds (2006)
Kucherov, Gregory, Noé, Laurent, Roytberg, Mihkail
We propose a general approach to compute the seed sensitivity, that can be applied to different definitions of seeds. It treats separately three components of the seed sensitivity problem -- a set of...
A unifying framework for seed sensitivity and its application to subset seeds (2006)
Kucherov, Gregory, Noé, Laurent, Roytberg, Mihkail
We propose a general approach to compute the seed sensitivity, that can be applied to different definitions of seeds. It treats separately three components of the seed sensitivity problem -- a set of...
A unifying framework for seed sensitivity and its application to subset seeds (2006)
Kucherov, Gregory, Noé, Laurent, Roytberg, Mihkail
We propose a general approach to compute the seed sensitivity, that can be applied to different definitions of seeds. It treats separately three components of the seed sensitivity problem -- a set of...
A unifying framework for seed sensitivity and its application to subset seeds (2006)
Kucherov, Gregory, Noé, Laurent, Roytberg, Mihkail
We propose a general approach to compute the seed sensitivity, that can be applied to different definitions of seeds. It treats separately three components of the seed sensitivity problem -- a set of...
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, ...
A unifying framework for seed sensitivity and its application to subset seeds (2006)
Gregory Kucherov, Laurent Noé, Mikhail Roytberg
We propose a general approach to compute the seed sensitivity, that can be applied to different definitions of seeds. It treats separately three components of the seed sensitivity problem â a...
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...
Les méthodes de recherche de similarités les plus fréquemment utilisées dans le cadre de la génomique sont heuristiques.Elles se basent sur un principe de filtrage du texte qui permet de...
Les méthodes de recherche de similarités les plus fréquemment utilisées dans le cadre de la génomique sont heuristiques.Elles se basent sur un principe de filtrage du texte qui permet de...
YASS: enhancing the sensitivity of DNA similarity search (2005)
Noé, Laurent, Kucherov, Gregory
YASS is a DNA local alignment tool based on an efficient and sensitive filtering algorithm. It applies transition-constrained seeds to specify the most probable conserved motifs between homologous...
YASS: enhancing the sensitivity of DNA similarity search (2005)
Noé, Laurent, Kucherov, Gregory
YASS is a DNA local alignment tool based on an efficient and sensitive filtering algorithm. It applies transition-constrained seeds to specify the most probable conserved motifs between homologous...
Multi-seed lossless filtration (2005)
Kucherov, Gregory, Noé, Laurent, Roytberg, Mikhail
We study a method of seed-based lossless filtration for approximate string matching and related bioinformatics applications. The method is based on a simultaneous use of several spaced seeds rather...
Multi-seed lossless filtration (2005)
Kucherov, Gregory, Noé, Laurent, Roytberg, Mikhail
We study a method of seed-based lossless filtration for approximate string matching and related bioinformatics applications. The method is based on a simultaneous use of several spaced seeds rather...
A Unifying Framework for Seed Sensitivity and Its Application to Subset Seeds (2005)
Kucherov, Gregory, Noé, Laurent, Roytberg, Mihkail
We propose a general approach to compute the seed sensitivity, that can be applied to different definitions of seeds. It treats separately three components of the seed sensitivity problem -- a set 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...
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...
Les méthodes de recherche de similarités les plus fréquemment utilisées dans le cadre de la génomique sont heuristiques. Elles se basent sur un principe de filtrage du texte qui permet de...
Les méthodes de recherche de similarités les plus fréquemment utilisées dans le cadre de la génomique sont heuristiques. Elles se basent sur un principe de filtrage du texte qui permet de...
Les méthodes de recherche de similarités les plus fréquemment utilisées dans le cadre de la génomique sont heuristiques. Elles se basent sur un principe de filtrage du texte qui permet de...
Multiseed Lossless Filtration (2005)
Kucherov, Gregory, Noé, Laurent, Roytberg, Mikhail
We study a method of seed-based lossless filtration for approximate string matching and related bioinformatics applications. The method is based on a simultaneous use of several spaced seeds rather...
Multiseed Lossless Filtration (2005)
Kucherov, Gregory, Noé, Laurent, Roytberg, Mikhail
We study a method of seed-based lossless filtration for approximate string matching and related bioinformatics applications. The method is based on a simultaneous use of several spaced seeds rather...
YASS: enhancing the sensitivity of DNA similarity (2005)
YASS is a DNA local alignment tool based on an efficient and sensitive filtering algorithm. It applies transition-constrained seeds to specify the most probable conserved motifs between homologous...
Gregory Kucherov, Laurent Noé, Mikhail Roytberg
We propose a general approach to compute the seed sensitivity, that can be applied to di#erent definitions of seeds. It treats separately three components of the seed sensitivity problem -- a set of...
Gregory Kucherov, Laurent Noé, Mikhail Roytberg
We propose a general approach to compute the seed sensitivity, that can be applied to different definitions of seeds. It treats separately three components of the seed sensitivity problem -- a set of...
Multiseed Lossless Filtration (2005)
Gregory Kucherov, Laurent Noé, Mikhail Roytberg
We study a method of seed-based lossless filtration for approximate string matching and related bioinformatics applications. The method is based on a simultaneous use of several spaced seeds rather...
Les méthodes de recherche de similarités les plus fréquemment utilisées dans le cadre de la génomique sont heuristiques. Elles se basent sur un principe de filtrage du texte qui permet de...
Multiseed lossless filtration (2005)
Gregory Kucherov, Laurent Noé, Mikhail Roytberg
We study a method of seed-based lossless filtration for approximate string matching and related bioinformatics applications. The method is based on a simultaneous use of several spaced seeds rather...
YASS: enhancing the sensitivity of DNA similarity search (2005)
Noé, Laurent, Kucherov, Gregory
YASS is a DNA local alignment tool based on an efficient and sensitive filtering algorithm. It applies transition-constrained seeds to specify the most probable conserved motifs between homologous...
A unifying framework for seed sensitivity and its application to subset seeds (2004)
Kucherov, Gregory, Noé, Laurent, Roytberg, Mikhail
We propose a general approach to compute the seed sensitivity, that can be applied to different definitions of seeds. It treats separately three components of the seed sensitivity problem -- a set...
Improved hit criteria for DNA local alignment (2004)
Noé, Laurent, Kucherov, Gregory
Abstract Background The hit criterion is a key component of heuristic local alignment algorithms. It specifies a class of patterns assumed to witness a potential similarity, and this choice is...
Multi-seed lossless filtration (Extended abstract) (2004)
Kucherov, Gregory, Noé, Laurent, Roytberg, Mikhail
We study a method of seed-based lossless ltration for approximate string matching and related applications. The method is based on a simultaneous use of several spaced seeds rather than a single seed...
Multi-seed lossless filtration (Extended abstract) (2004)
Kucherov, Gregory, Noé, Laurent, Roytberg, Mikhail
We study a method of seed-based lossless ltration for approximate string matching and related applications. The method is based on a simultaneous use of several spaced seeds rather than a single seed...
A unifying framework for seed sensitivity and its application to subset seeds (2004)
Kucherov, Gregory, Noé, Laurent, Roytberg, Mikhail
We propose a general approach to compute the seed sensitivity, that can be applied to different definitions of seeds. It treats separately three components of the seed sensitivity problem -- a set of...
A unifying framework for seed sensitivity and its application to subset seeds (2004)
Kucherov, Gregory, Noé, Laurent, Roytberg, Mikhail
We propose a general approach to compute the seed sensitivity, that can be applied to different definitions of seeds. It treats separately three components of the seed sensitivity problem -- a set of...
Multi-seed lossless filtration (Extended abstract) (2004)
Kucherov, Gregory, Noé, Laurent, Roytberg, Mikhail
We study a method of seed-based lossless ltration for approximate string matching and related applications. The method is based on a simultaneous use of several spaced seeds rather than a single seed...
Multi-seed lossless filtration (Extended abstract) (2004)
Gregory Kucherov, Laurent Noé, Mikhail Roytberg
We study a method of seed-based lossless filtration for approximate string matching and related applications. The method is based on a simultaneous use of several spaced seeds rather than a single...
Multi-seed lossless filtration (Extended abstract) (2004)
Gregory Kucherov, Laurent Noé, Mikhail Roytberg
We study a method of seed-based lossless filtration for approximate string matching and related applications. The method is based on a simultaneous use of several spaced seeds rather than a single...
Estimating Seed Sensitivity on Homogeneous Alignments (2004)
Gregory Kucherov, Laurent Noé, Yann Ponty
We address the problem of estimating the sensitivity of seed-based similarity search algorithms. In contrast to approaches based on Markov models [18, 6, 3, 4, 10], we study the estimation based on...
Improved hit criteria for DNA local alignment (2004)
The hit criterion is a key component of heuristic local alignment algorithms. It specifies a class of patterns assumed to witness a potential similarity, and this choice is decisive for the...
Improved hit criteria for DNA local alignment (2004)
Background: The hit criterion is a key component of heuristic local alignment algorithms. It specifies a class of patterns assumed to witness a potential similarity, and this choice is decisive for...
Improved hit criteria for DNA local alignment (2004)
The hit criterion is a key component of heuristic local alignment algorithms. It specifies a class of patterns assumed to witness a potential similarity, and this choice is decisive for the...
Estimating seed sensitivity on homogeneous alignments (2003)
Kucherov, Gregory, Noé, Laurent, Ponty, Yann
We address the problem of measuring the sensitivity of seed-based similarity search algorithms. In contrast to approaches based on Markov models, we study the measurement based on homogeneous...
YASS: Similarity search in DNA sequences (2003)
Noé, Laurent, Kucherov, Gregory
We describe YASS -- a new tool for finding local similarities in DNA sequences. The YASS algorithm first scans the sequence(s) and creates on the fly groups of (small exact repeats obtained by...
Estimating seed sensitivity on homogeneous alignments (2003)
Kucherov, Gregory, Noé, Laurent, Ponty, Yann
We address the problem of measuring the sensitivity of seed-based similarity search algorithms. In contrast to approaches based on Markov models, we study the measurement based on homogeneous...
YASS: Similarity search in DNA sequences (2003)
Noé, Laurent, Kucherov, Gregory
We describe YASS -- a new tool for finding local similarities in DNA sequences. The YASS algorithm first scans the sequence(s) and creates on the fly groups of (small exact repeats obtained by...
YASS: Similarity search in DNA sequences (2003)
Noé, Laurent, Kucherov, Gregory
We describe YASS -- a new tool for finding local similarities in DNA sequences. The YASS algorithm first scans the sequence(s) and creates on the fly groups of (small exact repeats obtained by...
Estimating seed sensitivity on homogeneous alignments (2003)
Kucherov, Gregory, Noé, Laurent, Ponty, Yann
We address the problem of measuring the sensitivity of seed-based similarity search algorithms. In contrast to approaches based on Markov models, we study the measurement based on homogeneous...
YASS: Similarity search in DNA sequences (2003)
We describe YASS – a new tool for finding local similarities in DNA sequences. The YASS algorithm first scans the sequence(s) and creates on the fly groups of seeds (small exact repeats obtained by...
YASS: Similarity search in DNA sequences (2003)
Identifying similarity regions inside a DNA sequence (repeats), or between two sequences (local alignment), is a fundamental problem in bioinformatics. For this task, many algorithms use a technique...
Estimating seed sensitivity on homogeneous alignments (2003)
Gregory Kucherov, Laurent Noé, Yann Ponty
We address the problem of measuring the sensitivity of seed-based similarity search algorithms. In contrast to approaches based on Markov models, we study the measurement based on homogeneous...
A new method of finding similarity regions in DNA sequences (2002)
Identifying similarity regions inside a DNA sequence (repeats), or between two sequences (local alignment), is a fundamental problem in bioinformatics. For this task, many algorithms use a technique...
YASS: enhancing the sensitivity of DNA similarity search
Noé, Laurent, Kucherov, Gregory
YASS is a DNA local alignment tool based on an efficient and sensitive filtering algorithm. It applies transition-constrained seeds to specify the most probable conserved motifs between homologous...
YASS: enhancing the sensitivity of DNA similarity search
Noé, Laurent, Kucherov, Gregory
YASS is a DNA local alignment tool based on an efficient and sensitive filtering algorithm. It applies transition-constrained seeds to specify the most probable conserved motifs between homologous...