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Blast sampling for structural and functional analyses

Anne Friedrich, Raymond Ripp, Nicolas Garnier, Emmanuel Bettler, Gilbert Deléage, Olivier Poch, Luc Moulinier
2007 BMC Bioinformatics  
The post-genomic era is characterised by a torrent of biological information flooding the public databases. As a direct consequence, similarity searches starting with a single query sequence frequently lead to the identification of hundreds, or even thousands of potential homologues. The huge volume of data renders the subsequent structural, functional and evolutionary analyses very difficult. It is therefore essential to develop new strategies for efficient sampling of this large sequence
more » ... , in order to reduce the number of sequences to be processed. At the same time, it is important to retain the most pertinent sequences for structural and functional studies. An exhaustive analysis on a large scale test set (284 protein families) was performed to compare the efficiency of four different sampling methods aimed at selecting the most pertinent sequences. These four methods sample the proteins detected by BlastP searches and can be divided into two categories: two customisable methods where the user defines either the maximal number or the percentage of sequences to be selected; two automatic methods in which the number of sequences selected is determined by the program. We focused our analysis on the potential information content of the sampled sets of sequences using multiple alignment of complete sequences as the main validation tool. The study considered two criteria: the total number of sequences in BlastP and their associated E-values. The subsequent analyses investigated the influence of the sampling methods on the E-value distributions, the sequence coverage, the final multiple alignment quality and the active site characterisation at various residue conservation thresholds as a function of these criteria. The comparative analysis of the four sampling methods allows us to propose a suitable sampling strategy that significantly reduces the number of homologous sequences required for alignment, while at the same time maintaining the relevant information concerning the active site residues.
doi:10.1186/1471-2105-8-62 pmid:17319945 pmcid:PMC1819393 fatcat:zjlolskhfndtrkezmqaecuol5y

Potential role of the X circular code in the regulation of gene expression [article]

Julie Thompson, Raymond Ripp, Claudine Mayer, Olivier Poch, Christian J. Michel
2020 bioRxiv   pre-print
The X circular code is a set of 20 trinucleotides (codons) that has been identified in the protein-coding genes of most organisms (bacteria, archaea, eukaryotes, plasmids, viruses). It has been shown previously that the X circular code has the important mathematical property of being an error-correcting code. Thus, motifs of the X circular code, i.e. a series of codons belonging to X , which are significantly enriched in the genes, allow identification and maintenance of the reading frame in
more » ... es. X motifs have also been identified in many transfer RNA (tRNA) genes and in important functional regions of the ribosomal RNA (rRNA), notably in the peptidyl transferase center and the decoding center. Here, we investigate the potential role of X motifs as functional elements in the regulation of gene expression. Surprisingly, the definition of a simple parameter identifies several relations between the X circular code and gene expression. First, we identify a correlation between the 20 codons of the X circular code and the optimal codons/dicodons that have been shown to influence translation efficiency. Using previously published experimental data, we then demonstrate that the presence of X motifs in genes can be used to predict the level of gene expression. Based on these observations, we propose the hypothesis that the X motifs represent a new genetic signal, contributing to the maintenance of the correct reading frame and the optimization and regulation of gene expression.
doi:10.1101/2020.03.23.003251 fatcat:36xlkrde6zevvgekwzox2xpuz4

PARSEC: PAtteRn SEarch and Contextualization

Alexis Allot, Yannick-Noël Anno, Laetitia Poidevin, Raymond Ripp, Olivier Poch, Odile Lecompte
2013 Computer applications in the biosciences : CABIOS  
We present PARSEC (PAtteRn Search and Contextualization), a new open source platform for guided discovery, allowing localization and biological characterization of short genomic sites in entire eukaryotic genomes. PARSEC can search for a sequence or a degenerated pattern. The retrieved set of genomic sites can be characterized in terms of (i) conservation in model organisms, (ii) genomic context (proximity to genes) and (iii) function of neighboring genes. These modules allow the user to
more » ... , visualize, filter and extract biological knowledge from a set of short genomic regions such as transcription factor binding sites. Availability: Web site implemented in Java, JavaScript and Cþþ, with all major browsers supported. Freely available at Source code is freely available at
doi:10.1093/bioinformatics/btt455 pmid:23929031 fatcat:4a5dz23e3zcaph75slvnovi6ku

OrthoInspector 3.0: open portal for comparative genomics

Yannis Nevers, Arnaud Kress, Audrey Defosset, Raymond Ripp, Benjamin Linard, Julie D Thompson, Olivier Poch, Odile Lecompte
2018 Nucleic Acids Research  
OrthoInspector is one of the leading software suites for orthology relations inference. In this paper, we describe a major redesign of the OrthoInspector online resource along with a significant increase in the number of species: 4753 organisms are now covered across the three domains of life, making OrthoInspector the most exhaustive orthology resource to date in terms of covered species (excluding viruses). The new website integrates original data exploration and visualization tools in an
more » ... nomic interface. Distributions of protein orthologs are represented by heatmaps summarizing their evolutionary histories, and proteins with similar profiles can be directly accessed. Two novel tools have been implemented for comparative genomics: a phylogenetic profile search that can be used to find proteins with a specific presence-absence profile and investigate their functions and, inversely, a GO profiling tool aimed at deciphering evolutionary histories of molecular functions, processes or cell components. In addition to the re-designed website, the OrthoInspector resource now provides a REST interface for programmatic access. OrthoInspector 3.0 is available at
doi:10.1093/nar/gky1068 pmid:30380106 pmcid:PMC6323921 fatcat:dhx4n4gcxffrhf3fgcyf4geinm

Functional insights into the core-TFIIH from a comparative survey

Florence Bedez, Benjamin Linard, Xavier Brochet, Raymond Ripp, Julie D. Thompson, Dino Moras, Odile Lecompte, Olivier Poch
2013 Genomics  
TFIIH is a eukaryotic complex composed of two subcomplexes, the CAK (Cdk activating kinase) and the core-TFIIH. The core-TFIIH, composed of seven subunits (XPB, XPD, P62, P52, P44, P34, and P8), plays a crucial role in transcription and repair. Here, we performed an extended sequence analysis to establish the accurate phylogenetic distribution of the core-TFIIH in 63 eukaryotic organisms. In spite of the high conservation of the seven subunits at the sequence and genomic levels, the
more » ... c P8, P34, P52 and P62 are absent from one or a few unicellular species. To gain insight into their respective roles, we undertook a comparative genomic analysis of the whole proteome to identify the gene sets sharing similar presence/absence patterns. While little information was inferred for P8 and P62, our studies confirm the known role of P52 in repair and suggest for the first time the implication of the core TFIIH in mRNA splicing via P34.
doi:10.1016/j.ygeno.2012.11.003 pmid:23147676 fatcat:2zihtbq5wbhutfmx53bx7raicm

BAliBASE 3.0: Latest developments of the multiple sequence alignment benchmark

Julie D. Thompson, Patrice Koehl, Raymond Ripp, Olivier Poch
2005 Proteins: Structure, Function, and Bioinformatics  
Multiple sequence alignment is one of the cornerstones of modern molecular biology. It is used to identify conserved motifs, to determine protein domains, in 2D/3D structure prediction by homology and in evolutionary studies. Recently, high-throughput technologies such as genome sequencing and structural proteomics have lead to an explosion in the amount of sequence and structure information available. In response, several new multiple alignment methods have been developed that improve both the
more » ... efficiency and the quality of protein alignments. Consequently, the benchmarks used to evaluate and compare these methods must also evolve. We present here the latest release of the most widely used multiple alignment benchmark, BAliBASE, which provides high quality, manually refined, reference alignments based on 3D structural superpositions. Version 3.0 of BAliBASE includes new, more challenging test cases, representing the real problems encountered when aligning large sets of complex sequences. Using a novel, semiautomatic update protocol, the number of protein families in the benchmark has been increased and representative test cases are now available that cover most of the protein fold space. The total number of proteins in BAliBASE has also been significantly increased from 1444 to 6255 sequences. In addition, full-length sequences are now provided for all test cases, which represent difficult cases for both global and local alignment programs. Finally, the BAliBASE Web site ( has been completely redesigned to provide a more user-friendly, interactive interface for the visualization of the BAliBASE reference alignments and the associated annotations. Proteins 2005;61:127-136.
doi:10.1002/prot.20527 pmid:16044462 fatcat:3c4jqdg2onasppytyasau4s7wq

OrthoInspector 2.0: Software and database updates

Benjamin Linard, Alexis Allot, Raphaël Schneider, Can Morel, Raymond Ripp, Marc Bigler, Julie D. Thompson, Olivier Poch, Odile Lecompte
2014 Computer applications in the biosciences : CABIOS  
We previously developed OrthoInspector, a software suite incorporating an original algorithm for the rapid detection of orthology and inparalogy relations between different species. We have added new functional tools and considerably extended the databases of pre-computed orthology/inparalogy relationships. Availability: Software and databases are freely available at
doi:10.1093/bioinformatics/btu642 pmid:25273105 fatcat:tmq66b2rsndixamqs2vnbqeyly

Integrated Annotation and Analysis of In Situ Hybridization Images Using the ImAnno System: Application to the Ear and Sensory Organs of the Fetal Mouse

Raymond Romand, Raymond Ripp, Laetitia Poidevin, Marcel Boeglin, Lars Geffers, Pascal Dollé, Olivier Poch, Olivia Bermingham-McDonogh
2015 PLoS ONE  
An in situ hybridization (ISH) study was performed on 2000 murine genes representing around 10% of the protein-coding genes present in the mouse genome using data generated by the EURExpress consortium. This study was carried out in 25 tissues of late gestation embryos (E14.5), with a special emphasis on the developing ear and on five distinct developing sensory organs, including the cochlea, the vestibular receptors, the sensory retina, the olfactory organ, and the vibrissae follicles. The
more » ... lts obtained from an analysis of more than 11,000 micrographs have been integrated in a newly developed knowledgebase, called ImAnno. In addition to managing the multilevel micrograph annotations performed by human experts, ImAnno provides public access to various integrated databases and tools. Thus, it facilitates the analysis of complex ISH gene expression patterns, as well as functional annotation and interaction of gene sets. It also provides direct links to human pathways and diseases. Hierarchical clustering of expression patterns in the 25 tissues revealed three main branches corresponding to tissues with common functions and/or embryonic origins. To illustrate the integrative power of ImAnno, we explored the expression, function and disease traits of the sensory epithelia of the five presumptive sensory organs. The study identified 623 genes (out of 2000) concomitantly expressed in the five embryonic epithelia, among which many (*12%) were involved in human disorders. Finally, various multilevel interaction networks were characterized, highlighting differential functional enrichments of directly or indirectly interacting genes. These analyses exemplify an under-represention of "sensory" functions in the sensory gene set suggests that E14.5 is a pivotal stage between the developmental stage and the functional phase that will be fully reached only after birth.
doi:10.1371/journal.pone.0118024 pmid:25706271 pmcid:PMC4338146 fatcat:dy4bqdln5nbafpsukl7w6pps3e

RETINOBASE: a web database, data mining and analysis platform for gene expression data on retina

Ravi Kalathur, Nicolas Gagniere, Guillaume Berthommier, Laetitia Poidevin, Wolfgang Raffelsberger, Raymond Ripp, Thierry Léveillard, Olivier Poch
2008 BMC Genomics  
The retina is a multi-layered sensory tissue that lines the back of the eye and acts at the interface of input light and visual perception. Its main function is to capture photons and convert them into electrical impulses that travel along the optic nerve to the brain where they are turned into images. It consists of neurons, nourishing blood vessels and different cell types, of which neural cells predominate. Defects in any of these cells can lead to a variety of retinal diseases, including
more » ... -related macular degeneration, retinitis pigmentosa, Leber congenital amaurosis and glaucoma. Recent progress in genomics and microarray technology provides extensive opportunities to examine alterations in retinal gene expression profiles during development and diseases. However, there is no specific database that deals with retinal gene expression profiling. In this context we have built RETINOBASE, a dedicated microarray database for retina. Description: RETINOBASE is a microarray relational database, analysis and visualization system that allows simple yet powerful queries to retrieve information about gene expression in retina. It provides access to gene expression metadata and offers significant insights into gene networks in retina, resulting in better hypothesis framing for biological problems that can subsequently be tested in the laboratory. Public and proprietary data are automatically analyzed with 3 distinct methods, RMA, dChip and MAS5, then clustered using 2 different K-means and 1 mixture models method. Thus, RETINOBASE provides a framework to compare these methods and to optimize the retinal data analysis. RETINOBASE has three different modules, "Gene Information", "Raw Data System Analysis" and "Fold change system Analysis" that are interconnected in a relational schema, allowing efficient retrieval and cross comparison of data. Currently, RETINOBASE contains datasets from 28 different microarray experiments performed in 5 different model systems: drosophila, zebrafish, rat, mouse and human. The database is supported by a platform that is designed to easily integrate new functionalities and is also frequently updated. Conclusion: The results obtained from various biological scenarios can be visualized, compared and downloaded. The results of a case study are presented that highlight the utility of RETINOBASE. Overall, RETINOBASE provides efficient access to the global expression profiling of retinal genes from different organisms under various conditions.
doi:10.1186/1471-2164-9-208 pmid:18457592 pmcid:PMC2386825 fatcat:eaxtw4npp5cfnl25aodrgcy72y

MyGeneFriends: A Social Network Linking Genes, Genetic Diseases, and Researchers

Alexis Allot, Kirsley Chennen, Yannis Nevers, Laetitia Poidevin, Arnaud Kress, Raymond Ripp, Julie Dawn Thompson, Olivier Poch, Odile Lecompte
2017 Journal of Medical Internet Research  
The constant and massive increase of biological data offers unprecedented opportunities to decipher the function and evolution of genes and their roles in human diseases. However, the multiplicity of sources and flow of data mean that efficient access to useful information and knowledge production has become a major challenge. This challenge can be addressed by taking inspiration from Web 2.0 and particularly social networks, which are at the forefront of big data exploration and human-data
more » ... raction. Objective: MyGeneFriends is a Web platform inspired by social networks, devoted to genetic disease analysis, and organized around three types of proactive agents: genes, humans, and genetic diseases. The aim of this study was to improve exploration and exploitation of biological, postgenomic era big data. Methods: MyGeneFriends leverages conventions popularized by top social networks (Facebook, LinkedIn, etc), such as networks of friends, profile pages, friendship recommendations, affinity scores, news feeds, content recommendation, and data visualization. Results: MyGeneFriends provides simple and intuitive interactions with data through evaluation and visualization of connections (friendships) between genes, humans, and diseases. The platform suggests new friends and publications and allows agents to follow the activity of their friends. It dynamically personalizes information depending on the user's specific interests and provides an efficient way to share information with collaborators. Furthermore, the user's behavior itself generates new information that constitutes an added value integrated in the network, which can be used to discover new connections between biological agents. Conclusions: We have developed MyGeneFriends, a Web platform leveraging conventions from popular social networks to redefine the relationship between humans and biological big data and improve human processing of biomedical data. MyGeneFriends is available at Allot et al JOURNAL OF MEDICAL INTERNET RESEARCH XSL • FO RenderX add new information, via micro-blogging for example; (2) spread information through the network via sharing [2]; (3) evaluate information with like, dislike, or vote reactions; (4) partition information using privacy settings; or (5) annotate information with comments. Agents play an active role in the evolution of the network structure by creating nodes (agent profile pages) and bidirectional (friendship) or unidirectional (follower) links between agents. They also partition agents into groups and connect agents to unstructured information (tagging). These actions are processed by specialized tools embedded in the network to create valuable feedback in the form of filtered and personalized information such as friendship suggestions, affinity scores between people, news feeds, targeted advertisements [3], merchandise suggestions [4], or real-time world observations [5] .
doi:10.2196/jmir.6676 pmid:28623182 pmcid:PMC5493784 fatcat:456chxeijfbcrmq36fyai5oc44

Conjugating effects of symbionts and environmental factors on gene expression in deep-sea hydrothermal vent mussels

Isabelle Boutet, Raymond Ripp, Odile Lecompte, Carole Dossat, Erwan Corre, Arnaud Tanguy, François H Lallier
2011 BMC Genomics  
The deep-sea hydrothermal vent mussel Bathymodiolus azoricus harbors thiotrophic and methanotrophic symbiotic bacteria in its gills. While the symbiotic relationship between this hydrothermal mussel and these chemoautotrophic bacteria has been described, the molecular processes involved in the cross-talking between symbionts and host, in the maintenance of the symbiois, in the influence of environmental parameters on gene expression, and in transcriptome variation across individuals remain
more » ... y understood. In an attempt to understand how, and to what extent, this double symbiosis affects host gene expression, we used a transcriptomic approach to identify genes potentially regulated by symbiont characteristics, environmental conditions or both. This study was done on mussels from two contrasting populations. Results: Subtractive libraries allowed the identification of about 1000 genes putatively regulated by symbiosis and/ or environmental factors. Microarray analysis showed that 120 genes (3.5% of all genes) were differentially expressed between the Menez Gwen (MG) and Rainbow (Rb) vent fields. The total number of regulated genes in mussels harboring a high versus a low symbiont content did not differ significantly. With regard to the impact of symbiont content, only 1% of all genes were regulated by thiotrophic (SOX) and methanotrophic (MOX) bacteria content in MG mussels whereas 5.6% were regulated in mussels collected at Rb. MOX symbionts also impacted a higher proportion of genes than SOX in both vent fields. When host transcriptome expression was analyzed with respect to symbiont gene expression, it was related to symbiont quantity in each field. Conclusions: Our study has produced a preliminary description of a transcriptomic response in a hydrothermal vent mussel host of both thiotrophic and methanotrophic symbiotic bacteria. This model can help to identify genes involved in the maintenance of symbiosis or regulated by environmental parameters. Our results provide evidence of symbiont effect on transcriptome regulation, with differences related to type of symbiont, even though the relative percentage of genes involved remains limited. Differences observed between the vent site indicate that environment strongly influences transcriptome regulation and impacts both activity and relative abundance of each symbiont. Among all these genes, those participating in recognition, the immune system, oxidative stress, and energy metabolism constitute new promising targets for extended studies on symbiosis and the effect of environmental parameters on the symbiotic relationships in B. azoricus.
doi:10.1186/1471-2164-12-530 pmid:22034982 pmcid:PMC3218092 fatcat:wseirl3wtbcavorwggwq2oiele

Introduction du nouveau centre de données biomédicales Décrypthon

Hoan Nguyen, Guillaume Berthommier, Anne Friedrich, Laetitia Poidevin, Raymond Ripp, Luc Moulinier, Olivier Poch, Association ARIA (Association Pour La Recherche D'Informations Et Applications)
2008 Conférence en Recherche d'Infomations et Applications  
This paper presents the design and the implementation of the new high performance biomedical data center of the Décrypthon computing grid which provides a strong potential for calculation and storage to high trhoughput biological applications and projects. In order to efficiently share the biological data required by the application, the Décrypthon data center is integrated in the computing grid to provide local databases of nucleotide, genomic and proteomic sequences. In addition, the access
more » ... methods for heterogeneous and distributeddata, and treatment of joint queries, analysis and visualization are provided. A new system of data integration, called BIRD (for Biological Integration and Retrieval of Data), considered as the core of the Décrypthon data center, was developed to locally integrate very large genomic, proteomic and transcriptomic datasets. BIRD also provides an engine and a high level query language allowing the biologist to extract pertinent information. MOTS-CLÉS : base de données biologiques, intégration des données, bioinformatique, langage de requêtes biologique, BIRD-QL, grille Décrypthon.
doi:10.24348/coria.2008.151 dblp:conf/coria/NguyenBFPRMP08 fatcat:6u2o73ku6vfbfldfigjwtyoxsa

Structural Genomics of Eukaryotic Targets at a Laboratory Scale

Didier Busso, Pierre Poussin-Courmontagne, David Rosé, Raymond Ripp, Alain Litt, Jean-Claude Thierry, Dino Moras
2005 Journal of Structural and Functional Genomics  
Ripp, manuscript in preparation).  ...  Ripp, manuscript in preparation and], and to clone selected sequences into multiple expression vectors for protein production using mainly Escherichia coli as expression  ... 
doi:10.1007/s10969-005-1909-6 pmid:16211503 fatcat:chhj5bw57jdwhmnslsxmqhvnom

KD4v: comprehensible knowledge discovery system for missense variant

Tien-Dao Luu, Alin Rusu, Vincent Walter, Benjamin Linard, Laetitia Poidevin, Raymond Ripp, Luc Moulinier, Jean Muller, Wolfgang Raffelsberger, Nicolas Wicker, Odile Lecompte, Julie D. Thompson (+2 others)
2012 Nucleic Acids Research  
A major challenge in the post-genomic era is a better understanding of how human genetic alterations involved in disease affect the gene products. The KD4v (Comprehensible Knowledge Discovery System for Missense Variant) server allows to characterize and predict the phenotypic effects (deleterious/neutral) of missense variants. The server provides a set of rules learned by Induction Logic Programming (ILP) on a set of missense variants described by conservation, physico-chemical, functional and
more » ... 3D structure predicates. These rules are interpretable by non-expert humans and are used to accurately predict the deleterious/neutral status of an unknown mutation. The web server is available at
doi:10.1093/nar/gks474 pmid:22641855 pmcid:PMC3394327 fatcat:w3ri226mdbfsllra5tay3rsbfu
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