Integration of Exploration and Search: A Case Study of the M3 Model

International audienceEffective support for multimedia analytics applications requires exploration and search to be integrated seamlessly into a single interaction model. Media metadata can be seen as defining a multidimensional media space, casting multimedia analytics tasks as exploration, manipulation and augmentation of that space. We present an initial case study of integrating exploration and search within this multidimensional media space. We extend the M3 model, initially proposed as a pure exploration tool, and show that it can be elegantly extended to allow searching within an exploration context and exploring within a search context. We then evaluate the suitability of relational database management systems, as representatives of today’s data management technologies, for implementing the extended M3 model. Based on our results, we finally propose some research directions for scalability of multimedia analytics

Databases of homologous gene families for comparative genomics

International audienceBackground: Comparative genomics is a central step in many sequence analysis studies, from gene annotation and the identification of new functional regions in genomes, to the study of evolutionary processes at the molecular level (speciation, single gene or whole genome duplications, etc.) and phylogenetics. In that context, databases providing users high quality homologous families and sequence alignments as well as phylogenetic trees based on state of the art algorithms are becoming indispensable. Methods: We developed an automated procedure allowing massive all-against-all similarity searches, gene clustering, multiple alignments computation, and phylogenetic trees construction and reconciliation. The application of this procedure to a very large set of sequences is possible through parallel computing on a large computer cluster. Results: Three databases were developed using this procedure: HOVERGEN, HOGENOM and HOMOLENS. These databases share the same architecture but differ in their content. HOVERGEN contains sequences from vertebrates, HOGENOM is mainly devoted to completely sequenced microbial organisms, and HOMOLENS is devoted to metazoan genomes from Ensembl. Access to the databases is provided through Web query forms, a general retrieval system and a client-server graphical interface. The later can be used to perform tree-pattern based searches allowing, among other uses, to retrieve sets of orthologous genes. The three databases, as well as the software required to build and query them, can be used or downloaded from the PBIL (Pôle Bioinformatique Lyonnais) site at http://pbil.univ-lyon1.fr/

RegExpBlasting (REB), a Regular Expression Blasting algorithm based on multiply aligned sequences

Background: One of the most frequent uses of bioinformatics tools concerns functional characterization of a newly produced nucleotide sequence (a query sequence) by applying Blast or FASTA against a set of sequences (the subject sequences). However, in some specific contexts, it is useful to compare the query sequence against a cluster such as a MultiAlignment (MA). We present here the RegExpBlasting (REB) algorithm, which compares an unclassified sequence with a dataset of patterns defined by application of Regular Expression rules to a given-as-input MA datasets. The REB algorithm workflow consists in i. the definition of a dataset of multialignments ii. the association of each MA to a pattern, defined by application of regular expression rules; iii. automatic characterization of a submitted biosequence according to the function of the sequences described by the pattern best matching the query sequence. Results: An application of this algorithm is used in the "characterize your sequence" tool available in the PPNEMA resource. PPNEMA is a resource of Ribosomal Cistron sequences from various species, grouped according to nematode genera. It allows the retrieval of plant nematode multialigned sequences or the classification of new nematode rDNA sequences by applying REB. The same algorithm also supports automatic updating of the PPNEMA database. The present paper gives examples of the use of REB within PPNEMA. Conclusion: The use of REB in PPNEMA updating, the PPNEMA "characterize your sequence" option clearly demonstrates the power of the method. Using REB can also rapidly solve any other bioinformatics problem, where the addition of a new sequence to a pre-existing cluster is required. The statistical tests carried out here show the powerful flexibility of the method

PhEVER: a database for the global exploration of virus–host evolutionary relationships

Fast viral adaptation and the implication of this rapid evolution in the emergence of several new infectious diseases have turned this issue into a major challenge for various research domains. Indeed, viruses are involved in the development of a wide range of pathologies and understanding how viruses and host cells interact in the context of adaptation remains an open question. In order to provide insights into the complex interactions between viruses and their host organisms and namely in the acquisition of novel functions through exchanges of genetic material, we developed the PhEVER database. This database aims at providing accurate evolutionary and phylogenetic information to analyse the nature of virus–virus and virus–host lateral gene transfers. PhEVER (http://pbil.univ-lyon1.fr/databases/phever) is a unique database of homologous families both (i) between sequences from different viruses and (ii) between viral sequences and sequences from cellular organisms. PhEVER integrates extensive data from up-to-date completely sequenced genomes (2426 non-redundant viral genomes, 1007 non-redundant prokaryotic genomes, 43 eukaryotic genomes ranging from plants to vertebrates) and offers a clustering of proteins into homologous families containing at least one viral sequences, as well as alignments and phylogenies for each of these families. Public access to PhEVER is available through its webpage and through all dedicated ACNUC retrieval systems

RecPhyloXML: a format for reconciled gene trees.

A reconciliation is an annotation of the nodes of a gene tree with evolutionary events-for example, speciation, gene duplication, transfer, loss, etc.-along with a mapping onto a species tree. Many algorithms and software produce or use reconciliations but often using different reconciliation formats, regarding the type of events considered or whether the species tree is dated or not. This complicates the comparison and communication between different programs. Here, we gather a consortium of software developers in gene tree species tree reconciliation to propose and endorse a format that aims to promote an integrative-albeit flexible-specification of phylogenetic reconciliations. This format, named recPhyloXML, is accompanied by several tools such as a reconciled tree visualizer and conversion utilities. http://phylariane.univ-lyon1.fr/recphyloxml/

Synthèse de nucléo-amphiphiles glycosylés et études de leurs comportements en présence et en absence d'acide nucléique

AVIGNON-BU Centrale (840072102) / SudocSudocFranceF

Développements d'outils pour l'aide à l'identification dans les grandes banques de familles de gènes

Le nombre de séquences génomiques disponibles augmente très vite du développement de méthodes de séquençage massif. La classification de ces séquences est nécessaire et permet l'étude de leurs relations évolutives. Des outils bioinformatiques automatisés sont indispensables pour effectuer ces opérations d'identification de façon précise et rapide. Nous avons développé HoSeqI (Homologous Sequence Identification), un système permettant d'automatiser l'identification de séquences dans de grandes banques de familles de gènes homologues. HoSeqI propose une interface accessible sur internet (http://pbil.univ-lyon1.fr/software/HoSeqI/) afin d'identifier une séquence et de visualiser l'alignement et la phylogénie obtenus. Un autre programme, dérivé d'HoSeqI, a été implémenté pour l'ajout automatique de séquences génomiques aux banques de familles. Enfin, un travail sur l'identification automatique de séquences bactériennes d'ARN 16S et la détection de séquences chimères a été effectuéLYON1-BU.Sciences (692662101) / SudocSudocFranceF