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description Publicationkeyboard_double_arrow_right Part of book or chapter of book 2018 FrancePublisher:Springer International Publishing Authors: Arzalluz-Luque, Angeles; Devailly, Guillaume; Joshi, Anagha;Arzalluz-Luque, Angeles; Devailly, Guillaume; Joshi, Anagha;Single cell RNA sequencing is becoming increasingly popular due to rapidly evolving technology, decreasing costs and its wide applicability. However, the technology suffers from high drop-out rate and high technical noise, mainly due to the low starting material. This hinders the extraction of biological variability, or signal, from the data. One of the first steps in the single cell analysis pipelines is, therefore, to filter the data to keep the most informative features only. This filtering step is often done by arbitrarily selecting a threshold.
https://doi.org/10.1... arrow_drop_down https://doi.org/10.1007/978-3-...Part of book or chapter of book . 2018 . Peer-reviewedLicense: Springer TDMData sources: CrossrefMémoires en Sciences de l'Information et de la Communication; Hal-DiderotPart of book or chapter of book . 2018add ClaimPlease grant OpenAIRE to access and update your ORCID works.This Research product is the result of merged Research products in OpenAIRE.
You have already added works in your ORCID record related to the merged Research product.This Research product is the result of merged Research products in OpenAIRE.
You have already added works in your ORCID record related to the merged Research product.All Research productsarrow_drop_down <script type="text/javascript"> <!-- document.write('<div id="oa_widget"></div>'); document.write('<script type="text/javascript" src="https://www.openaire.eu/index.php?option=com_openaire&view=widget&format=raw&projectId=10.1007/978-3-319-78723-7_31&type=result"></script>'); --> </script>
For further information contact us at helpdesk@openaire.eu0 citations 0 popularity Average influence Average impulse Average Powered by BIP!more_vert https://doi.org/10.1... arrow_drop_down https://doi.org/10.1007/978-3-...Part of book or chapter of book . 2018 . Peer-reviewedLicense: Springer TDMData sources: CrossrefMémoires en Sciences de l'Information et de la Communication; Hal-DiderotPart of book or chapter of book . 2018add ClaimPlease grant OpenAIRE to access and update your ORCID works.This Research product is the result of merged Research products in OpenAIRE.
You have already added works in your ORCID record related to the merged Research product.This Research product is the result of merged Research products in OpenAIRE.
You have already added works in your ORCID record related to the merged Research product.All Research productsarrow_drop_down <script type="text/javascript"> <!-- document.write('<div id="oa_widget"></div>'); document.write('<script type="text/javascript" src="https://www.openaire.eu/index.php?option=com_openaire&view=widget&format=raw&projectId=10.1007/978-3-319-78723-7_31&type=result"></script>'); --> </script>
For further information contact us at helpdesk@openaire.eudescription Publicationkeyboard_double_arrow_right Part of book or chapter of book 2019 FrancePublisher:Springer New York Authors: Andrei, Oana; Fernández, Maribel; Kirchner, Hélène; Pinaud, Bruno;Andrei, Oana; Fernández, Maribel; Kirchner, Hélène; Pinaud, Bruno;International audience; This chapter presents Porgy—an interactive visual environment for rule-based modelling of biochemical systems. We model molecules and molecule interactions as port graphs and port graph rewrite rules, respectively. We use rewriting strategies to control which rules to apply, and where and when to apply them. Our main contributions to rule-based modelling of biochemical systems lie in the strategy language and the associated visual and interactive features offered by Porgy. These features facilitate an exploratory approach to test different ways of applying the rules while recording the model evolution, and tracking and plotting parameters. We illustrate Porgy’s features with a study of the role of a scaffold protein in RAF/MEK/ERK signalling.
Hal-Diderot arrow_drop_down Hal-DiderotPart of book or chapter of book . 2019https://doi.org/10.1007/978-1-...Part of book or chapter of book . 2019 . Peer-reviewedLicense: Springer TDMData sources: CrossrefINRIA a CCSD electronic archive server; Mémoires en Sciences de l'Information et de la CommunicationPart of book or chapter of book . 2019Full-Text: https://hal.science/hal-01429890/documentadd ClaimPlease grant OpenAIRE to access and update your ORCID works.This Research product is the result of merged Research products in OpenAIRE.
You have already added works in your ORCID record related to the merged Research product.This Research product is the result of merged Research products in OpenAIRE.
You have already added works in your ORCID record related to the merged Research product.All Research productsarrow_drop_down <script type="text/javascript"> <!-- document.write('<div id="oa_widget"></div>'); document.write('<script type="text/javascript" src="https://www.openaire.eu/index.php?option=com_openaire&view=widget&format=raw&projectId=10.1007/978-1-4939-9102-0_3&type=result"></script>'); --> </script>
For further information contact us at helpdesk@openaire.eu1 citations 1 popularity Average influence Average impulse Average Powered by BIP!more_vert Hal-Diderot arrow_drop_down Hal-DiderotPart of book or chapter of book . 2019https://doi.org/10.1007/978-1-...Part of book or chapter of book . 2019 . Peer-reviewedLicense: Springer TDMData sources: CrossrefINRIA a CCSD electronic archive server; Mémoires en Sciences de l'Information et de la CommunicationPart of book or chapter of book . 2019Full-Text: https://hal.science/hal-01429890/documentadd ClaimPlease grant OpenAIRE to access and update your ORCID works.This Research product is the result of merged Research products in OpenAIRE.
You have already added works in your ORCID record related to the merged Research product.This Research product is the result of merged Research products in OpenAIRE.
You have already added works in your ORCID record related to the merged Research product.All Research productsarrow_drop_down <script type="text/javascript"> <!-- document.write('<div id="oa_widget"></div>'); document.write('<script type="text/javascript" src="https://www.openaire.eu/index.php?option=com_openaire&view=widget&format=raw&projectId=10.1007/978-1-4939-9102-0_3&type=result"></script>'); --> </script>
For further information contact us at helpdesk@openaire.eudescription Publicationkeyboard_double_arrow_right Conference object , Part of book or chapter of book 2014 FrancePublisher:Springer International Publishing Authors: Belleannée, Catherine; Sallou, Olivier; Nicolas, Jacques;Belleannée, Catherine; Sallou, Olivier; Nicolas, Jacques;Most of the current practice of pattern matching tools is oriented towards finding efficient ways to compare sequences. This is useful but insufficient: as the knowledge and understanding of some functional or structural aspects of living systems improve, analysts in molecular biology progressively shift from mere classification tasks to modeling tasks. People need to be able to express global sequence architectures and check various hypotheses on the way their sequences are structured. It appears necessary to offer generic tools for this task, allowing to build more expressive models of biological sequence families, on the basis of their content and structure. This article introduces Logol, a new application designed to achieve pattern matching in possibly large sequences with customized biological patterns. Logol consists in both a language for describing patterns, and the associated parser for effective pattern search in sequences (RNA, DNA or protein) with such patterns. The Logol language, based on an high level grammatical formalism, allows to express flexible patterns (with mispairings and indels) composed of both sequential elements (such as motifs) and structural elements (such as repeats or pseudoknots). Its expressive power is presented through an application using the main components of the language : the identification of -1 programmed ribosomal frameshifting (PRF) events in messenger RNA sequences. Logol allows the design of sophisticated patterns, and their search in large nucleic or amino acid sequences. It is available on the GenOuest bioinformatics platform at http://logol.genouest.org. The core application is a command-line application, available for different operating systems. The Logol suite also includes interfaces, e.g. an interface for graphically drawing the pattern.
https://link.springe... arrow_drop_down HAL-Rennes 1; Hal-DiderotConference object . 2014Full-Text: https://hal.inria.fr/hal-01059506/documenthttps://doi.org/10.1007/978-3-...Part of book or chapter of book . 2014 . Peer-reviewedData sources: Crossrefadd ClaimPlease grant OpenAIRE to access and update your ORCID works.This Research product is the result of merged Research products in OpenAIRE.
You have already added works in your ORCID record related to the merged Research product.This Research product is the result of merged Research products in OpenAIRE.
You have already added works in your ORCID record related to the merged Research product.All Research productsarrow_drop_down <script type="text/javascript"> <!-- document.write('<div id="oa_widget"></div>'); document.write('<script type="text/javascript" src="https://www.openaire.eu/index.php?option=com_openaire&view=widget&format=raw&projectId=10.1007/978-3-319-09192-1_4&type=result"></script>'); --> </script>
For further information contact us at helpdesk@openaire.euAccess Routesbronze 2 citations 2 popularity Average influence Average impulse Average Powered by BIP!more_vert https://link.springe... arrow_drop_down HAL-Rennes 1; Hal-DiderotConference object . 2014Full-Text: https://hal.inria.fr/hal-01059506/documenthttps://doi.org/10.1007/978-3-...Part of book or chapter of book . 2014 . Peer-reviewedData sources: Crossrefadd ClaimPlease grant OpenAIRE to access and update your ORCID works.This Research product is the result of merged Research products in OpenAIRE.
You have already added works in your ORCID record related to the merged Research product.This Research product is the result of merged Research products in OpenAIRE.
You have already added works in your ORCID record related to the merged Research product.All Research productsarrow_drop_down <script type="text/javascript"> <!-- document.write('<div id="oa_widget"></div>'); document.write('<script type="text/javascript" src="https://www.openaire.eu/index.php?option=com_openaire&view=widget&format=raw&projectId=10.1007/978-3-319-09192-1_4&type=result"></script>'); --> </script>
For further information contact us at helpdesk@openaire.eudescription Publicationkeyboard_double_arrow_right Conference object , Report , Part of book or chapter of book 2005 FrancePublisher:Springer Berlin Heidelberg Authors: Coste, François; Kerbellec, Goulven;Coste, François; Kerbellec, Goulven;doi: 10.1007/11564096_50
We propose here to learn automata for the characterization of proteins families to overcome the limitations of the position-specific characterizations classically used in Pattern Discovery. We introduce a new heuristic approach learning non-deterministic automata based on selection and ordering of significantly similar fragments to be merged and on physico-chemical properties identification. Quality of the characterization of the major intrinsic protein (MIP) family is assessed by leave-one-out cross-validation for a large range of models specificity. // Nous proposons d'apprendre des automates caractérisant des familles de protéines pour dépasser les limites des méthodes usuelles de Découverte de Motifs qui sont actuellement restreintes à des caractérisations par positions. Nous introduisons ainsi une nouvelle approche heuristique permettant d'apprendre des automates non déterministes, basée sur la sélection, le tri et la fusion de fragments significativement similaires, ainsi que sur l'identification de propriétés physico-chimiques. La qualité de caractérisation de la famille de protéines MIP (major intrinsic protein) est attestée par validation croisée de type leave-one-out pour différents niveaux de spécificité des modèles.
https://link.springe... arrow_drop_down https://doi.org/10.1007/115640...Part of book or chapter of book . 2005 . Peer-reviewedLicense: Springer TDMData sources: CrossrefHAL-Rennes 1; Hal-DiderotConference object . 2005Full-Text: https://hal.inria.fr/hal-03405434/documentadd ClaimPlease grant OpenAIRE to access and update your ORCID works.This Research product is the result of merged Research products in OpenAIRE.
You have already added works in your ORCID record related to the merged Research product.This Research product is the result of merged Research products in OpenAIRE.
You have already added works in your ORCID record related to the merged Research product.All Research productsarrow_drop_down <script type="text/javascript"> <!-- document.write('<div id="oa_widget"></div>'); document.write('<script type="text/javascript" src="https://www.openaire.eu/index.php?option=com_openaire&view=widget&format=raw&projectId=10.1007/11564096_50&type=result"></script>'); --> </script>
For further information contact us at helpdesk@openaire.euAccess Routesbronze 10 citations 10 popularity Average influence Average impulse Average Powered by BIP!more_vert https://link.springe... arrow_drop_down https://doi.org/10.1007/115640...Part of book or chapter of book . 2005 . Peer-reviewedLicense: Springer TDMData sources: CrossrefHAL-Rennes 1; Hal-DiderotConference object . 2005Full-Text: https://hal.inria.fr/hal-03405434/documentadd ClaimPlease grant OpenAIRE to access and update your ORCID works.This Research product is the result of merged Research products in OpenAIRE.
You have already added works in your ORCID record related to the merged Research product.This Research product is the result of merged Research products in OpenAIRE.
You have already added works in your ORCID record related to the merged Research product.All Research productsarrow_drop_down <script type="text/javascript"> <!-- document.write('<div id="oa_widget"></div>'); document.write('<script type="text/javascript" src="https://www.openaire.eu/index.php?option=com_openaire&view=widget&format=raw&projectId=10.1007/11564096_50&type=result"></script>'); --> </script>
For further information contact us at helpdesk@openaire.eudescription Publicationkeyboard_double_arrow_right Conference object , Part of book or chapter of book 2014 FrancePublisher:Springer International Publishing Authors: Lemaitre, Claire; Ciortuz, Liviu; Peterlongo, Pierre;Lemaitre, Claire; Ciortuz, Liviu; Peterlongo, Pierre;International audience; We propose a formal model and an algorithm for detecting inversion breakpoints without a reference genome, directly from raw NGS data. This model is characterized by a fixed size topological pattern in the de Bruijn Graph. We describe precisely the possible sources of false pos- itives and false negatives and we additionally propose a sequence-based filter giving a good trade-off between precision and recall of the method. We implemented these ideas in a prototype called TakeABreak. Ap- plied on simulated inversions in genomes of various complexity (from E. coli to a human chromosome dataset), TakeABreak provided promising results with a low memory footprint and a small computational time.
https://hal.inria.fr... arrow_drop_down Hal-DiderotConference object . 2014Full-Text: https://hal.inria.fr/hal-01063157v3/documentData sources: Hal-Diderothttps://doi.org/10.1007/978-3-...Part of book or chapter of book . 2014 . Peer-reviewedData sources: Crossrefadd ClaimPlease grant OpenAIRE to access and update your ORCID works.This Research product is the result of merged Research products in OpenAIRE.
You have already added works in your ORCID record related to the merged Research product.This Research product is the result of merged Research products in OpenAIRE.
You have already added works in your ORCID record related to the merged Research product.All Research productsarrow_drop_down <script type="text/javascript"> <!-- document.write('<div id="oa_widget"></div>'); document.write('<script type="text/javascript" src="https://www.openaire.eu/index.php?option=com_openaire&view=widget&format=raw&projectId=10.1007/978-3-319-07953-0_10&type=result"></script>'); --> </script>
For further information contact us at helpdesk@openaire.eu10 citations 10 popularity Average influence Average impulse Top 10% Powered by BIP!more_vert https://hal.inria.fr... arrow_drop_down Hal-DiderotConference object . 2014Full-Text: https://hal.inria.fr/hal-01063157v3/documentData sources: Hal-Diderothttps://doi.org/10.1007/978-3-...Part of book or chapter of book . 2014 . Peer-reviewedData sources: Crossrefadd ClaimPlease grant OpenAIRE to access and update your ORCID works.This Research product is the result of merged Research products in OpenAIRE.
You have already added works in your ORCID record related to the merged Research product.This Research product is the result of merged Research products in OpenAIRE.
You have already added works in your ORCID record related to the merged Research product.All Research productsarrow_drop_down <script type="text/javascript"> <!-- document.write('<div id="oa_widget"></div>'); document.write('<script type="text/javascript" src="https://www.openaire.eu/index.php?option=com_openaire&view=widget&format=raw&projectId=10.1007/978-3-319-07953-0_10&type=result"></script>'); --> </script>
For further information contact us at helpdesk@openaire.eudescription Publicationkeyboard_double_arrow_right Part of book or chapter of book 2009 FrancePublisher:Springer Berlin Heidelberg Funded by:AKA | Algorithms for Genomic Se...AKA| Algorithms for Genomic Search ProblemsRivals , Eric; Salmela , Leena; Kalsi , Petri; Kiiskinen , Petteri; Tarhio , Jorma;International audience; With Next Generation Sequencers, sequence based transcriptomic or epigenomic assays yield millions of short sequence reads that need to map back on a reference genome. The upcoming versions of these sequencers promise even higher sequencing capacities; this may turn the read mapping task into a bottleneck for which alternative pattern matching approaches must be experimented. We present an algorithm and its implementation, called MPSCAN, which uses a sophisticated filtration scheme to match a set patterns/reads exactly on a sequence. MPSCAN can search for millions of reads in a single pass through the genome without indexing its sequence. Moreover, we show that MPSCAN offers an optimal average time complexity, which is sublinear in the text length, meaning that it does not need to examine all sequence positions. Comparisons with BLAT-like tools and with specialised read mapping programs (like BOWTIE or ZOOM) demonstrate that MPSCAN also is the fastest algorithm in practice for exact matching. Our accuracy and scalability reveal that some tool are inappropriate for read mapping. Moreover, we provide evidence suggesting that exact matching may be a valuable solution in some read mapping applications. As most read mapping programs somehow rely on exact matching procedures to perform approximate pattern mapping, the filtration scheme we experimented may reveal useful in the design of future algorithms. The absence of genome index gives MPSCAN its low memory requirement and flexibility that let it to run on a desktop computer, and avoids a time-consuming genome preprocessing.
HAL Descartes; HAL-P... arrow_drop_down HAL Descartes; HAL-Pasteur; HAL-Inserm; Mémoires en Sciences de l'Information et de la Communication; Hal-DiderotPart of book or chapter of book . Conference object . 2009https://doi.org/10.1007/978-3-...Part of book or chapter of book . 2009 . Peer-reviewedLicense: Springer TDMData sources: Crossrefadd ClaimPlease grant OpenAIRE to access and update your ORCID works.This Research product is the result of merged Research products in OpenAIRE.
You have already added works in your ORCID record related to the merged Research product.This Research product is the result of merged Research products in OpenAIRE.
You have already added works in your ORCID record related to the merged Research product.All Research productsarrow_drop_down <script type="text/javascript"> <!-- document.write('<div id="oa_widget"></div>'); document.write('<script type="text/javascript" src="https://www.openaire.eu/index.php?option=com_openaire&view=widget&format=raw&projectId=10.1007/978-3-642-04241-6_21&type=result"></script>'); --> </script>
For further information contact us at helpdesk@openaire.eu17 citations 17 popularity Average influence Average impulse Top 10% Powered by BIP!more_vert HAL Descartes; HAL-P... arrow_drop_down HAL Descartes; HAL-Pasteur; HAL-Inserm; Mémoires en Sciences de l'Information et de la Communication; Hal-DiderotPart of book or chapter of book . Conference object . 2009https://doi.org/10.1007/978-3-...Part of book or chapter of book . 2009 . Peer-reviewedLicense: Springer TDMData sources: Crossrefadd ClaimPlease grant OpenAIRE to access and update your ORCID works.This Research product is the result of merged Research products in OpenAIRE.
You have already added works in your ORCID record related to the merged Research product.This Research product is the result of merged Research products in OpenAIRE.
You have already added works in your ORCID record related to the merged Research product.All Research productsarrow_drop_down <script type="text/javascript"> <!-- document.write('<div id="oa_widget"></div>'); document.write('<script type="text/javascript" src="https://www.openaire.eu/index.php?option=com_openaire&view=widget&format=raw&projectId=10.1007/978-3-642-04241-6_21&type=result"></script>'); --> </script>
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description Publicationkeyboard_double_arrow_right Part of book or chapter of book 2018 FrancePublisher:Springer International Publishing Authors: Arzalluz-Luque, Angeles; Devailly, Guillaume; Joshi, Anagha;Arzalluz-Luque, Angeles; Devailly, Guillaume; Joshi, Anagha;Single cell RNA sequencing is becoming increasingly popular due to rapidly evolving technology, decreasing costs and its wide applicability. However, the technology suffers from high drop-out rate and high technical noise, mainly due to the low starting material. This hinders the extraction of biological variability, or signal, from the data. One of the first steps in the single cell analysis pipelines is, therefore, to filter the data to keep the most informative features only. This filtering step is often done by arbitrarily selecting a threshold.
https://doi.org/10.1... arrow_drop_down https://doi.org/10.1007/978-3-...Part of book or chapter of book . 2018 . Peer-reviewedLicense: Springer TDMData sources: CrossrefMémoires en Sciences de l'Information et de la Communication; Hal-DiderotPart of book or chapter of book . 2018add ClaimPlease grant OpenAIRE to access and update your ORCID works.This Research product is the result of merged Research products in OpenAIRE.
You have already added works in your ORCID record related to the merged Research product.This Research product is the result of merged Research products in OpenAIRE.
You have already added works in your ORCID record related to the merged Research product.All Research productsarrow_drop_down <script type="text/javascript"> <!-- document.write('<div id="oa_widget"></div>'); document.write('<script type="text/javascript" src="https://www.openaire.eu/index.php?option=com_openaire&view=widget&format=raw&projectId=10.1007/978-3-319-78723-7_31&type=result"></script>'); --> </script>
For further information contact us at helpdesk@openaire.eu0 citations 0 popularity Average influence Average impulse Average Powered by BIP!more_vert https://doi.org/10.1... arrow_drop_down https://doi.org/10.1007/978-3-...Part of book or chapter of book . 2018 . Peer-reviewedLicense: Springer TDMData sources: CrossrefMémoires en Sciences de l'Information et de la Communication; Hal-DiderotPart of book or chapter of book . 2018add ClaimPlease grant OpenAIRE to access and update your ORCID works.This Research product is the result of merged Research products in OpenAIRE.
You have already added works in your ORCID record related to the merged Research product.This Research product is the result of merged Research products in OpenAIRE.
You have already added works in your ORCID record related to the merged Research product.All Research productsarrow_drop_down <script type="text/javascript"> <!-- document.write('<div id="oa_widget"></div>'); document.write('<script type="text/javascript" src="https://www.openaire.eu/index.php?option=com_openaire&view=widget&format=raw&projectId=10.1007/978-3-319-78723-7_31&type=result"></script>'); --> </script>
For further information contact us at helpdesk@openaire.eudescription Publicationkeyboard_double_arrow_right Part of book or chapter of book 2019 FrancePublisher:Springer New York Authors: Andrei, Oana; Fernández, Maribel; Kirchner, Hélène; Pinaud, Bruno;Andrei, Oana; Fernández, Maribel; Kirchner, Hélène; Pinaud, Bruno;International audience; This chapter presents Porgy—an interactive visual environment for rule-based modelling of biochemical systems. We model molecules and molecule interactions as port graphs and port graph rewrite rules, respectively. We use rewriting strategies to control which rules to apply, and where and when to apply them. Our main contributions to rule-based modelling of biochemical systems lie in the strategy language and the associated visual and interactive features offered by Porgy. These features facilitate an exploratory approach to test different ways of applying the rules while recording the model evolution, and tracking and plotting parameters. We illustrate Porgy’s features with a study of the role of a scaffold protein in RAF/MEK/ERK signalling.
Hal-Diderot arrow_drop_down Hal-DiderotPart of book or chapter of book . 2019https://doi.org/10.1007/978-1-...Part of book or chapter of book . 2019 . Peer-reviewedLicense: Springer TDMData sources: CrossrefINRIA a CCSD electronic archive server; Mémoires en Sciences de l'Information et de la CommunicationPart of book or chapter of book . 2019Full-Text: https://hal.science/hal-01429890/documentadd ClaimPlease grant OpenAIRE to access and update your ORCID works.This Research product is the result of merged Research products in OpenAIRE.
You have already added works in your ORCID record related to the merged Research product.This Research product is the result of merged Research products in OpenAIRE.
You have already added works in your ORCID record related to the merged Research product.All Research productsarrow_drop_down <script type="text/javascript"> <!-- document.write('<div id="oa_widget"></div>'); document.write('<script type="text/javascript" src="https://www.openaire.eu/index.php?option=com_openaire&view=widget&format=raw&projectId=10.1007/978-1-4939-9102-0_3&type=result"></script>'); --> </script>
For further information contact us at helpdesk@openaire.eu1 citations 1 popularity Average influence Average impulse Average Powered by BIP!more_vert Hal-Diderot arrow_drop_down Hal-DiderotPart of book or chapter of book . 2019https://doi.org/10.1007/978-1-...Part of book or chapter of book . 2019 . Peer-reviewedLicense: Springer TDMData sources: CrossrefINRIA a CCSD electronic archive server; Mémoires en Sciences de l'Information et de la CommunicationPart of book or chapter of book . 2019Full-Text: https://hal.science/hal-01429890/documentadd ClaimPlease grant OpenAIRE to access and update your ORCID works.This Research product is the result of merged Research products in OpenAIRE.
You have already added works in your ORCID record related to the merged Research product.This Research product is the result of merged Research products in OpenAIRE.
You have already added works in your ORCID record related to the merged Research product.All Research productsarrow_drop_down <script type="text/javascript"> <!-- document.write('<div id="oa_widget"></div>'); document.write('<script type="text/javascript" src="https://www.openaire.eu/index.php?option=com_openaire&view=widget&format=raw&projectId=10.1007/978-1-4939-9102-0_3&type=result"></script>'); --> </script>
For further information contact us at helpdesk@openaire.eudescription Publicationkeyboard_double_arrow_right Conference object , Part of book or chapter of book 2014 FrancePublisher:Springer International Publishing Authors: Belleannée, Catherine; Sallou, Olivier; Nicolas, Jacques;Belleannée, Catherine; Sallou, Olivier; Nicolas, Jacques;Most of the current practice of pattern matching tools is oriented towards finding efficient ways to compare sequences. This is useful but insufficient: as the knowledge and understanding of some functional or structural aspects of living systems improve, analysts in molecular biology progressively shift from mere classification tasks to modeling tasks. People need to be able to express global sequence architectures and check various hypotheses on the way their sequences are structured. It appears necessary to offer generic tools for this task, allowing to build more expressive models of biological sequence families, on the basis of their content and structure. This article introduces Logol, a new application designed to achieve pattern matching in possibly large sequences with customized biological patterns. Logol consists in both a language for describing patterns, and the associated parser for effective pattern search in sequences (RNA, DNA or protein) with such patterns. The Logol language, based on an high level grammatical formalism, allows to express flexible patterns (with mispairings and indels) composed of both sequential elements (such as motifs) and structural elements (such as repeats or pseudoknots). Its expressive power is presented through an application using the main components of the language : the identification of -1 programmed ribosomal frameshifting (PRF) events in messenger RNA sequences. Logol allows the design of sophisticated patterns, and their search in large nucleic or amino acid sequences. It is available on the GenOuest bioinformatics platform at http://logol.genouest.org. The core application is a command-line application, available for different operating systems. The Logol suite also includes interfaces, e.g. an interface for graphically drawing the pattern.
https://link.springe... arrow_drop_down HAL-Rennes 1; Hal-DiderotConference object . 2014Full-Text: https://hal.inria.fr/hal-01059506/documenthttps://doi.org/10.1007/978-3-...Part of book or chapter of book . 2014 . Peer-reviewedData sources: Crossrefadd ClaimPlease grant OpenAIRE to access and update your ORCID works.This Research product is the result of merged Research products in OpenAIRE.
You have already added works in your ORCID record related to the merged Research product.This Research product is the result of merged Research products in OpenAIRE.
You have already added works in your ORCID record related to the merged Research product.All Research productsarrow_drop_down <script type="text/javascript"> <!-- document.write('<div id="oa_widget"></div>'); document.write('<script type="text/javascript" src="https://www.openaire.eu/index.php?option=com_openaire&view=widget&format=raw&projectId=10.1007/978-3-319-09192-1_4&type=result"></script>'); --> </script>
For further information contact us at helpdesk@openaire.euAccess Routesbronze 2 citations 2 popularity Average influence Average impulse Average Powered by BIP!more_vert https://link.springe... arrow_drop_down HAL-Rennes 1; Hal-DiderotConference object . 2014Full-Text: https://hal.inria.fr/hal-01059506/documenthttps://doi.org/10.1007/978-3-...Part of book or chapter of book . 2014 . Peer-reviewedData sources: Crossrefadd ClaimPlease grant OpenAIRE to access and update your ORCID works.This Research product is the result of merged Research products in OpenAIRE.
You have already added works in your ORCID record related to the merged Research product.This Research product is the result of merged Research products in OpenAIRE.
You have already added works in your ORCID record related to the merged Research product.All Research productsarrow_drop_down <script type="text/javascript"> <!-- document.write('<div id="oa_widget"></div>'); document.write('<script type="text/javascript" src="https://www.openaire.eu/index.php?option=com_openaire&view=widget&format=raw&projectId=10.1007/978-3-319-09192-1_4&type=result"></script>'); --> </script>
For further information contact us at helpdesk@openaire.eudescription Publicationkeyboard_double_arrow_right Conference object , Report , Part of book or chapter of book 2005 FrancePublisher:Springer Berlin Heidelberg Authors: Coste, François; Kerbellec, Goulven;Coste, François; Kerbellec, Goulven;doi: 10.1007/11564096_50
We propose here to learn automata for the characterization of proteins families to overcome the limitations of the position-specific characterizations classically used in Pattern Discovery. We introduce a new heuristic approach learning non-deterministic automata based on selection and ordering of significantly similar fragments to be merged and on physico-chemical properties identification. Quality of the characterization of the major intrinsic protein (MIP) family is assessed by leave-one-out cross-validation for a large range of models specificity. // Nous proposons d'apprendre des automates caractérisant des familles de protéines pour dépasser les limites des méthodes usuelles de Découverte de Motifs qui sont actuellement restreintes à des caractérisations par positions. Nous introduisons ainsi une nouvelle approche heuristique permettant d'apprendre des automates non déterministes, basée sur la sélection, le tri et la fusion de fragments significativement similaires, ainsi que sur l'identification de propriétés physico-chimiques. La qualité de caractérisation de la famille de protéines MIP (major intrinsic protein) est attestée par validation croisée de type leave-one-out pour différents niveaux de spécificité des modèles.
https://link.springe... arrow_drop_down https://doi.org/10.1007/115640...Part of book or chapter of book . 2005 . Peer-reviewedLicense: Springer TDMData sources: CrossrefHAL-Rennes 1; Hal-DiderotConference object . 2005Full-Text: https://hal.inria.fr/hal-03405434/documentadd ClaimPlease grant OpenAIRE to access and update your ORCID works.This Research product is the result of merged Research products in OpenAIRE.
You have already added works in your ORCID record related to the merged Research product.This Research product is the result of merged Research products in OpenAIRE.
You have already added works in your ORCID record related to the merged Research product.All Research productsarrow_drop_down <script type="text/javascript"> <!-- document.write('<div id="oa_widget"></div>'); document.write('<script type="text/javascript" src="https://www.openaire.eu/index.php?option=com_openaire&view=widget&format=raw&projectId=10.1007/11564096_50&type=result"></script>'); --> </script>
For further information contact us at helpdesk@openaire.euAccess Routesbronze 10 citations 10 popularity Average influence Average impulse Average Powered by BIP!more_vert https://link.springe... arrow_drop_down https://doi.org/10.1007/115640...Part of book or chapter of book . 2005 . Peer-reviewedLicense: Springer TDMData sources: CrossrefHAL-Rennes 1; Hal-DiderotConference object . 2005Full-Text: https://hal.inria.fr/hal-03405434/documentadd ClaimPlease grant OpenAIRE to access and update your ORCID works.This Research product is the result of merged Research products in OpenAIRE.
You have already added works in your ORCID record related to the merged Research product.This Research product is the result of merged Research products in OpenAIRE.
You have already added works in your ORCID record related to the merged Research product.All Research productsarrow_drop_down <script type="text/javascript"> <!-- document.write('<div id="oa_widget"></div>'); document.write('<script type="text/javascript" src="https://www.openaire.eu/index.php?option=com_openaire&view=widget&format=raw&projectId=10.1007/11564096_50&type=result"></script>'); --> </script>
For further information contact us at helpdesk@openaire.eudescription Publicationkeyboard_double_arrow_right Conference object , Part of book or chapter of book 2014 FrancePublisher:Springer International Publishing Authors: Lemaitre, Claire; Ciortuz, Liviu; Peterlongo, Pierre;Lemaitre, Claire; Ciortuz, Liviu; Peterlongo, Pierre;International audience; We propose a formal model and an algorithm for detecting inversion breakpoints without a reference genome, directly from raw NGS data. This model is characterized by a fixed size topological pattern in the de Bruijn Graph. We describe precisely the possible sources of false pos- itives and false negatives and we additionally propose a sequence-based filter giving a good trade-off between precision and recall of the method. We implemented these ideas in a prototype called TakeABreak. Ap- plied on simulated inversions in genomes of various complexity (from E. coli to a human chromosome dataset), TakeABreak provided promising results with a low memory footprint and a small computational time.
https://hal.inria.fr... arrow_drop_down Hal-DiderotConference object . 2014Full-Text: https://hal.inria.fr/hal-01063157v3/documentData sources: Hal-Diderothttps://doi.org/10.1007/978-3-...Part of book or chapter of book . 2014 . Peer-reviewedData sources: Crossrefadd ClaimPlease grant OpenAIRE to access and update your ORCID works.This Research product is the result of merged Research products in OpenAIRE.
You have already added works in your ORCID record related to the merged Research product.This Research product is the result of merged Research products in OpenAIRE.
You have already added works in your ORCID record related to the merged Research product.All Research productsarrow_drop_down <script type="text/javascript"> <!-- document.write('<div id="oa_widget"></div>'); document.write('<script type="text/javascript" src="https://www.openaire.eu/index.php?option=com_openaire&view=widget&format=raw&projectId=10.1007/978-3-319-07953-0_10&type=result"></script>'); --> </script>
For further information contact us at helpdesk@openaire.eu10 citations 10 popularity Average influence Average impulse Top 10% Powered by BIP!more_vert https://hal.inria.fr... arrow_drop_down Hal-DiderotConference object . 2014Full-Text: https://hal.inria.fr/hal-01063157v3/documentData sources: Hal-Diderothttps://doi.org/10.1007/978-3-...Part of book or chapter of book . 2014 . Peer-reviewedData sources: Crossrefadd ClaimPlease grant OpenAIRE to access and update your ORCID works.This Research product is the result of merged Research products in OpenAIRE.
You have already added works in your ORCID record related to the merged Research product.This Research product is the result of merged Research products in OpenAIRE.
You have already added works in your ORCID record related to the merged Research product.All Research productsarrow_drop_down <script type="text/javascript"> <!-- document.write('<div id="oa_widget"></div>'); document.write('<script type="text/javascript" src="https://www.openaire.eu/index.php?option=com_openaire&view=widget&format=raw&projectId=10.1007/978-3-319-07953-0_10&type=result"></script>'); --> </script>
For further information contact us at helpdesk@openaire.eudescription Publicationkeyboard_double_arrow_right Part of book or chapter of book 2009 FrancePublisher:Springer Berlin Heidelberg Funded by:AKA | Algorithms for Genomic Se...AKA| Algorithms for Genomic Search ProblemsRivals , Eric; Salmela , Leena; Kalsi , Petri; Kiiskinen , Petteri; Tarhio , Jorma;International audience; With Next Generation Sequencers, sequence based transcriptomic or epigenomic assays yield millions of short sequence reads that need to map back on a reference genome. The upcoming versions of these sequencers promise even higher sequencing capacities; this may turn the read mapping task into a bottleneck for which alternative pattern matching approaches must be experimented. We present an algorithm and its implementation, called MPSCAN, which uses a sophisticated filtration scheme to match a set patterns/reads exactly on a sequence. MPSCAN can search for millions of reads in a single pass through the genome without indexing its sequence. Moreover, we show that MPSCAN offers an optimal average time complexity, which is sublinear in the text length, meaning that it does not need to examine all sequence positions. Comparisons with BLAT-like tools and with specialised read mapping programs (like BOWTIE or ZOOM) demonstrate that MPSCAN also is the fastest algorithm in practice for exact matching. Our accuracy and scalability reveal that some tool are inappropriate for read mapping. Moreover, we provide evidence suggesting that exact matching may be a valuable solution in some read mapping applications. As most read mapping programs somehow rely on exact matching procedures to perform approximate pattern mapping, the filtration scheme we experimented may reveal useful in the design of future algorithms. The absence of genome index gives MPSCAN its low memory requirement and flexibility that let it to run on a desktop computer, and avoids a time-consuming genome preprocessing.
HAL Descartes; HAL-P... arrow_drop_down HAL Descartes; HAL-Pasteur; HAL-Inserm; Mémoires en Sciences de l'Information et de la Communication; Hal-DiderotPart of book or chapter of book . Conference object . 2009https://doi.org/10.1007/978-3-...Part of book or chapter of book . 2009 . Peer-reviewedLicense: Springer TDMData sources: Crossrefadd ClaimPlease grant OpenAIRE to access and update your ORCID works.This Research product is the result of merged Research products in OpenAIRE.
You have already added works in your ORCID record related to the merged Research product.This Research product is the result of merged Research products in OpenAIRE.
You have already added works in your ORCID record related to the merged Research product.All Research productsarrow_drop_down <script type="text/javascript"> <!-- document.write('<div id="oa_widget"></div>'); document.write('<script type="text/javascript" src="https://www.openaire.eu/index.php?option=com_openaire&view=widget&format=raw&projectId=10.1007/978-3-642-04241-6_21&type=result"></script>'); --> </script>
For further information contact us at helpdesk@openaire.eu17 citations 17 popularity Average influence Average impulse Top 10% Powered by BIP!more_vert HAL Descartes; HAL-P... arrow_drop_down HAL Descartes; HAL-Pasteur; HAL-Inserm; Mémoires en Sciences de l'Information et de la Communication; Hal-DiderotPart of book or chapter of book . Conference object . 2009https://doi.org/10.1007/978-3-...Part of book or chapter of book . 2009 . Peer-reviewedLicense: Springer TDMData sources: Crossrefadd ClaimPlease grant OpenAIRE to access and update your ORCID works.This Research product is the result of merged Research products in OpenAIRE.
You have already added works in your ORCID record related to the merged Research product.This Research product is the result of merged Research products in OpenAIRE.
You have already added works in your ORCID record related to the merged Research product.All Research productsarrow_drop_down <script type="text/javascript"> <!-- document.write('<div id="oa_widget"></div>'); document.write('<script type="text/javascript" src="https://www.openaire.eu/index.php?option=com_openaire&view=widget&format=raw&projectId=10.1007/978-3-642-04241-6_21&type=result"></script>'); --> </script>
For further information contact us at helpdesk@openaire.eu