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Start Over Author "Université de Montpellier (UM)-Institut National de la Recherche Agronomique (INRA)-Institut National de Recherche en Informatique et en Automatique (Inria)-Centre National de la Recherche Scientifique (CNRS)" Journal bioinformatics
3 results on '"Université de Montpellier (UM)-Institut National de la Recherche Agronomique (INRA)-Institut National de Recherche en Informatique et en Automatique (Inria)-Centre National de la Recherche Scientifique (CNRS)"'

1. AQUAPONY: visualization and interpretation of phylogeographic information on phylogenetic trees

Author

Bastien Cazaux, Eric Rivals, Guillaume Castel, Méthodes et Algorithmes pour la Bioinformatique (MAB), Laboratoire d'Informatique de Robotique et de Microélectronique de Montpellier (LIRMM), Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS), Institut de Biologie Computationnelle (IBC), Institut National de la Recherche Agronomique (INRA)-Institut National de Recherche en Informatique et en Automatique (Inria)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS), Centre de Biologie pour la Gestion des Populations (UMR CBGP), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Université de Montpellier (UM)-Institut de Recherche pour le Développement (IRD [France-Sud])-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), ANR-11-BINF-0002,IBC,Institut de Biologie Computationnelle de Montpellier(2011), ANR-11-BINF-0002,IBC,Institut de biologie Computationnelle(2011), Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM), Université de Montpellier (UM)-Institut National de la Recherche Agronomique (INRA)-Institut National de Recherche en Informatique et en Automatique (Inria)-Centre National de la Recherche Scientifique (CNRS), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), and French National Research Agency (ANR) : ANR-11-BINF-0002

Subjects
Interactive visualisation, Statistics and Probability, Computer science, MESH: Biological Evolution G05.045.513, [SDV]Life Sciences [q-bio], analyse phylogénétique, computer.software_genre, Biochemistry, 03 medical and health sciences, Inference, Phylogenetics, Biologie animale, Molecular Biology, Phylogeny, 030304 developmental biology, Animal biology, 0303 health sciences, Phylogenetic tree, [SDV.BA]Life Sciences [q-bio]/Animal biology, 030302 biochemistry & molecular biology, Uncertainty, Probabilistic logic, [SDV.BIBS]Life Sciences [q-bio]/Quantitative Methods [q-bio.QM], Web, Computer Science Applications, Visualization, Phylogeography, Computational Mathematics, Tree (data structure), Phenotype, Computational Theory and Mathematics, arbre phylogénétique, Data mining, [INFO.INFO-BI]Computer Science [cs]/Bioinformatics [q-bio.QM], computer, Tree, Software
Abstract

Motivation The visualization and interpretation of evolutionary spatiotemporal scenarios is broadly and increasingly used in infectious disease research, ecology or agronomy. Using probabilistic frameworks, well-known tools can infer from molecular data ancestral traits for internal nodes in a phylogeny, and numerous phylogenetic rendering tools can display such evolutionary trees. However, visualizing such ancestral information and its uncertainty on the tree remains tedious. For instance, ancestral nodes can be associated to several geographical annotations with close probabilities and thus, several migration or transmission scenarios exist. Results We expose a web-based tool, named AQUAPONY, that facilitates such operations. Given an evolutionary tree with ancestral (e.g. geographical) annotations, the user can easily control the display of ancestral information on the entire tree or a subtree, and can view alternative phylogeographic scenarios along a branch according to a chosen uncertainty threshold. AQUAPONY interactively visualizes the tree and eases the objective interpretation of evolutionary scenarios. AQUAPONY’s implementation makes it highly responsive to user interaction, and instantaneously updates the tree visualizations even for large trees (which can be exported as image files). Availability and implementation AQUAPONY is coded in JavaScript/HTML, available under Cecill license, and can be freely used at http://www.atgc-montpellier.fr/aquapony/.

Published
2019

2. Tally: a scoring tool for boundary determination between repetitive and non-repetitive protein sequences

Author

Francois Richard, Ronnie Alves, Andrey V. Kajava, Centre de recherche en Biologie Cellulaire (CRBM), Université Montpellier 2 - Sciences et Techniques (UM2)-Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Université Montpellier 1 (UM1), Institut de Biologie Computationnelle (IBC), Institut National de la Recherche Agronomique (INRA)-Institut National de Recherche en Informatique et en Automatique (Inria)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS), Programa de Pós-Graduação em Ciências Contábeis [Belém, Brazil], Universidade Federal do Pará - UFPA [Belém, Brazil]-Instituto Tecnológico Vale [Belém, Brazil], National Research University of Information Technologies, Mechanics and Optics [St. Petersburg] (ITMO), Université Montpellier 1 (UM1)-Université Montpellier 2 - Sciences et Techniques (UM2)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS), Université de Montpellier (UM)-Institut National de la Recherche Agronomique (INRA)-Institut National de Recherche en Informatique et en Automatique (Inria)-Centre National de la Recherche Scientifique (CNRS), Centre de recherche en Biologie cellulaire de Montpellier (CRBM), Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS), and Federal University of Para - Universidade Federal do Pará - UFPA [Belém, Brazil] (UFPA)-Instituto Tecnológico Vale [Belém, Brazil] (ITV)

Subjects
0301 basic medicine, Statistics and Probability, Source code, Proteome, Sequence analysis, media_common.quotation_subject, [SDV.BC]Life Sciences [q-bio]/Cellular Biology, Biology, Biochemistry, Machine Learning, Set (abstract data type), 03 medical and health sciences, Tandem repeat, Sequence Analysis, Protein, Protein methods, [SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology, Amino Acid Sequence, Sensitivity (control systems), Molecular Biology, ComputingMilieux_MISCELLANEOUS, media_common, business.industry, Computational Biology, Proteins, Pattern recognition, Computer Science Applications, Computational Mathematics, 030104 developmental biology, Computational Theory and Mathematics, Tandem Repeat Sequences, Aperiodic graph, Benchmark (computing), Artificial intelligence, business, Algorithm, Algorithms
Abstract

Motivation: Tandem Repeats (TRs) are abundant in proteins, having a variety of fundamental functions. In many cases, evolution has blurred their repetitive patterns. This leads to the problem of distinguishing between sequences that contain highly imperfect TRs, and the sequences without TRs. The 3D structure of proteins can be used as a benchmarking criterion for TR detection in sequences, because the vast majority of proteins having TRs in sequences are built of repetitive 3D structural blocks. According to our benchmark, none of the existing scoring methods are able to clearly distinguish, based on the sequence analysis, between structures with and without 3D TRs. Results: We developed a scoring tool called Tally, which is based on a machine learning approach. Tally is able to achieve a better separation between sequences with structural TRs and sequences of aperiodic structures, than existing scoring procedures. It performs at a level of 81% sensitivity, while achieving a high specificity of 74% and an Area Under the Receiver Operating Characteristic Curve of 86%. Tally can be used to select a set of structurally and functionally meaningful TRs from all TRs detected in proteomes. The generated dataset is available for benchmarking purposes. Availability and implementation: Source code is available upon request. Tool and dataset can be accessed through our website: http://bioinfo.montp.cnrs.fr/?r=Tally. Contact: andrey.kajava@crbm.cnrs.fr Supplementary information: Supplementary data are available at Bioinformatics online.

Published
2016

3. SylvX: a viewer for phylogenetic tree reconciliations

Author

François Chevenet, Jean-Philippe Doyon, Edwin Jacox, Celine Scornavacca, Vincent Berry, Emmanuelle Jousselin, Institut de Biologie Computationnelle (IBC), Université de Montpellier (UM)-Institut National de la Recherche Agronomique (INRA)-Institut National de Recherche en Informatique et en Automatique (Inria)-Centre National de la Recherche Scientifique (CNRS), Du gène à l'écosystème (MIVEGEC-GeneSys), Pathogènes, Environnement, Santé Humaine (EPATH), Maladies infectieuses et vecteurs : écologie, génétique, évolution et contrôle (MIVEGEC), Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud])-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud])-Maladies infectieuses et vecteurs : écologie, génétique, évolution et contrôle (MIVEGEC), Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud])-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud]), Méthodes et Algorithmes pour la Bioinformatique (MAB), Laboratoire d'Informatique de Robotique et de Microélectronique de Montpellier (LIRMM), Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM), Institut des Sciences de l'Evolution de Montpellier (UMR ISEM), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-École pratique des hautes études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Montpellier (UM)-Institut de recherche pour le développement [IRD] : UR226-Centre National de la Recherche Scientifique (CNRS), Korean Research Institute of Bioscience , National Research Foundation of Korea, Ministry of Science, ICT & Future Planning , Biotechnology Research Initiative Program, Institut National de la Recherche Agronomique (INRA)-Institut National de Recherche en Informatique et en Automatique (Inria)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS), Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-École Pratique des Hautes Études (EPHE), Institut de Recherche pour le Développement (IRD [France-Sud])-Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-École pratique des hautes études (EPHE)-Université de Montpellier (UM)-Institut de recherche pour le développement [IRD] : UR226-Centre National de la Recherche Scientifique (CNRS), Chevenet, Francois, and Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud])

Subjects
0301 basic medicine, Statistics and Probability, arbre phylogénique, Theoretical computer science, Computer science, 0206 medical engineering, Economic shortage, 02 engineering and technology, [SDV.BID.SPT]Life Sciences [q-bio]/Biodiversity/Systematics, Phylogenetics and taxonomy, Network topology, computer.software_genre, Biochemistry, Evolution, Molecular, 03 medical and health sciences, Phylogenetics, Gene family, Molecular Biology, Gene, Phylogeny, Interpretation (logic), Phylogenetic tree, Computer Science Applications, Computational Mathematics, 030104 developmental biology, Computational Theory and Mathematics, Data mining, [INFO.INFO-BI]Computer Science [cs]/Bioinformatics [q-bio.QM], Host (network), computer, Software, 020602 bioinformatics
Abstract

Motivation: Reconciliation methods aim at recovering the evolutionary processes that shaped the history of a given gene family including events such as duplications, transfers and losses by comparing the discrepancies between the topologies of the associated gene and species trees. These methods are also used in the framework of host/parasite studies to recover co-diversification scenarios including co-speciation events, host-switches and extinctions. These evolutionary processes can be graphically represented as nested trees. These interconnected graphs can be visually messy and hard to interpret, and despite the fact that reconciliations are increasingly used, there is a shortage of tools dedicated to their graphical management. Here we present SylvX, a reconciliation viewer which implements classical phylogenetic graphic operators (swapping, highlighting, etc.) and new methods to ease interpretation and comparison of reconciliations (multiple maps, moving, shrinking sub-reconciliations). Availability and implementation: SylvX is an open source, cross-platform, standalone editor available for Windows and Unix-like systems including OSX. It is publicly available at www.sylvx.org. Contact: francois.chevenet@ird.fr

Published
2015

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