RPBS: a web resource for structural bioinformatics

RPBS (Ressource Parisienne en Bioinformatique Structurale) is a resource dedicated primarily to structural bioinformatics. It is the result of a joint effort by several teams to set up an interface that offers original and powerful methods in the field. As an illustration, we focus here on three such methods uniquely available at RPBS: AUTOMAT for sequence databank scanning, YAKUSA for structure databank scanning and WLOOP for homology loop modelling. The RPBS server can be accessed at and the specific services at

BioMart Central Portal: an open database network for the biological community

BioMart Central Portal is a first of its kind, community-driven effort to provide unified access to dozens of biological databases spanning genomics, proteomics, model organisms, cancer data, ontology information and more. Anybody can contribute an independently maintained resource to the Central Portal, allowing it to be exposed to and shared with the research community, and linking it with the other resources in the portal. Users can take advantage of the common interface to quickly utilize different sources without learning a new system for each. The system also simplifies cross-database searches that might otherwise require several complicated steps. Several integrated tools streamline common tasks, such as converting between ID formats and retrieving sequences. The combination of a wide variety of databases, an easy-to-use interface, robust programmatic access and the array of tools make Central Portal a one-stop shop for biological data querying. Here, we describe the structure of Central Portal and show example queries to demonstrate its capabilities

Contribution to the annotation of the chicken 20K oligo microarray of ARK-genomics

The chicken 20K oligo array provided by ARK-Genomics represents a very usefull tool for transcriptome analyses in the chicken. Because the 20460 70-mer oligo set was defined in 2004-2005 from heterogeneous data sources (http://www.ark-genomics.org), we checked the quality of the oligonucleotides, comparing them with the chromosomes of the 2.1 Washington University assembly of the Chicken Genome. This comparison was made using NCBI Blast 2 with a 75% similarity threshold over 50 base pairs. So we performed the annotation extraction only on the oligonucleotides found in a unique gene (even if it spanned on 2 exons). These annotations (Ensembl gene name, GO terms, orthologs, symbols corresponding to the human ortholog) were extracted from Ensembl using the blast HSP coordinates. Symbols for the human orthologs were validated with the HUGO gene nomenclature database using the GOret and HUGO_my_genes online tools (http://ouestgenopuces.univ-rennes1.fr/methodes_en.php). Other informations such as EC numbers and KEGG pathways IDs were extracted from bfind outputs and KEGG web pages. As results, among the 20460 gene-oligo, 13057 (64%) correspond to an unique coding region in a chicken genome sequence. From this oligo sub-set, only 32% presents an Ensembl gene name and/or a GO-biological process term. In contrast, 9360 (81%) presents a reliable human ortholog from which 1311 (14%) genes code enzymes. Among the 9360 genes, 7419 genes have a validated HUGO abbreviation, from which more GO terms could be extracted using different softwares (GOTM, Hugo-my-Genes) All bioinformatics procedures were developed by SIGENAE (INRA) and the results are available on site web: http://www.sigenae.org

Transcriptome Profiling Of Feeding-To-Fasting Transition In Chicken Liver Using A Chicken 20K Oligo Microarray

International audienceStarvation triggers a complex array of adaptative metabolic responses including energy-metabolic responses, a process which must imply tissue specific alterations in gene expression profiles. In the chicken, liver is a major organ controlling energy metabolism. The present study aimed to describe the evolution of global gene expression profiles in chicken liver during a 48h fasting period. Liver RNA samples were collected from 4 weeks old broilers, fed ad libitum or fasted for 16h or 48h. Following reverse-transcription and Cy dye labelling, the samples were hybridized on chicken 20K oligochips (ARK-genomics) against a reference sample. The data were then normalized by “Lowess-fitness” and analyzed by analysis of variance using LIMMA package. The number of genes altered by fasting increased from 190 at 16h to 611 at 48h (p<0.0001 following Benjamini-Hochberg correction) showing a more important hepatic transcriptional activity modification when the fasting was extended. After 16h of fasting, several genes involved in mitochondrial or peroxisomal fatty acid beta-oxidation (eight of the nine genes), in ketogenesis (three genes) and gluconeogenesis (three genes) were up-regulated, whereas genes involved in fatty acid synthesis (five genes) were down-regulated. This is consistent with the known regulation of glucose and lipid metabolisms in response to nutritional deprivation, as documented in different species. Further analysis was focused on 600 genes, which were significantly differentially expressed between at least two nutritional groups and for which a human ortholog could be identified, thus allowing to collect functional informations. This allowed identifying Gene Ontology categories and metabolic pathways altered by fasting