The ProDom database of protein domain families: more emphasis on 3D

ProDom is a comprehensive database of protein domain families generated from the global comparison of all available protein sequences. Recent improvements include the use of three-dimensional (3D) information from the SCOP database; a completely redesigned web interface (http://www.toulouse.inra.fr/prodom.html); visualization of ProDom domains on 3D structures; coupling of ProDom analysis with the Geno3D homology modelling server; Bayesian inference of evolutionary scenarios for ProDom families. In addition, we have developed ProDom-SG, a ProDom-based server dedicated to the selection of candidate proteins for structural genomics

Narcisse: a mirror view of conserved syntenies

New methods and tools are needed to exploit the unprecedented source of information made available by the completed and ongoing whole genome sequencing projects. The Narcisse database is dedicated to the study of genome conservation, from sequence similarities to conserved chromosomal segments or conserved syntenies, for a large number of animals, plants and bacterial completely sequenced genomes. The query interface, a comparative genome browser, enables to navigate between genome dotplots, comparative maps and sequence alignments. The Narcisse database can be accessed at http://narcisse.toulouse.inra.fr

InterPro, progress and status in 2005

InterPro, an integrated documentation resource of protein families, domains and functional sites, was created to integrate the major protein signature databases. Currently, it includes PROSITE, Pfam, PRINTS, ProDom, SMART, TIGRFAMs, PIRSF and SUPERFAMILY. Signatures are manually integrated into InterPro entries that are curated to provide biological and functional information. Annotation is provided in an abstract, Gene Ontology mapping and links to specialized databases. New features of InterPro include extended protein match views, taxonomic range information and protein 3D structure data. One of the new match views is the InterPro Domain Architecture view, which shows the domain composition of protein matches. Two new entry types were introduced to better describe InterPro entries: these are active site and binding site. PIRSF and the structure-based SUPERFAMILY are the latest member databases to join InterPro, and CATH and PANTHER are soon to be integrated. InterPro release 8.0 contains 11 007 entries, representing 2573 domains, 8166 families, 201 repeats, 26 active sites, 21 binding sites and 20 post-translational modification sites. InterPro covers over 78% of all proteins in the Swiss-Prot and TrEMBL components of UniProt. The database is available for text- and sequence-based searches via a webserver (http://www.ebi.ac.uk/interpro), and for download by anonymous FTP (ftp://ftp.ebi.ac.uk/pub/databases/interpro)

New developments in the InterPro database

InterPro is an integrated resource for protein families, domains and functional sites, which integrates the following protein signature databases: PROSITE, PRINTS, ProDom, Pfam, SMART, TIGRFAMs, PIRSF, SUPERFAMILY, Gene3D and PANTHER. The latter two new member databases have been integrated since the last publication in this journal. There have been several new developments in InterPro, including an additional reading field, new database links, extensions to the web interface and additional match XML files. InterPro has always provided matches to UniProtKB proteins on the website and in the match XML file on the FTP site. Additional matches to proteins in UniParc (UniProt archive) are now available for download in the new match XML files only. The latest InterPro release (13.0) contains more than 13 000 entries, covering over 78% of all proteins in UniProtKB. The database is available for text- and sequence-based searches via a webserver (), and for download by anonymous FTP (). The InterProScan search tool is now also available via a web service at

Digging for the spiny rat and hutia phylogeny using a gene capture approach, with the description of a new mammal subfamily

International audienceNext generation sequencing (NGS) and genomic database mining allow biologists to gather and select large molecular datasets well suited to address phylogenomics and molecular evolution questions. Here we applied this approach to a mammal family, the Echimyidae, for which generic relationships have been difficult to recover and often referred to as a star phylogeny. These South-American spiny rats represent a family of caviomorph rodents exhibiting a striking diversity of species and life history traits. Using a NGS exon capture protocol, we isolated and sequenced ca. 500 nuclear DNA exons for 35 species belonging to all major echimyid and capromyid clades. Exons were carefully selected to encompass as much diversity as possible in terms of rate of evolution, heterogeneity in the distribution of site-variation and nucleotide composition. Supermatrix inferences and coalescence-based approaches were subsequently applied to infer this family’s phylogeny. The inferred topologies were the same for both approaches, and support was maximal for each node, entirely resolving the ambiguous relationships of previous analyses. Fast-evolving nuclear exons tended to yield more reliable phylogenies, as slower-evolving sequences were not informative enough to disentangle the short branches of the Echimyidae radiation. Based on this resolved phylogeny and on molecular and morphological evidence, we confirm the rank of the Caribbean hutias – formerly placed in the Capromyidae family – as Capromyinae, a clade nested within Echimyidae. We also name and define Carterodontinae, a new subfamily of Echimyidae, comprising the extant monotypic genus Carterodon from Brazil, which is the closest living relative of West Indies Capromyinae

CALLISTO: a Semantics-Based Platform for Sharing FAIR Scientific Data

International audienceIn this paper, the platform CALLISTO (CALmip Launches an Interface for a Semantic Toolbox Online, https://callisto.calmip.univ-toulouse.fr/) is presented, aiming at open science construction around semantic description of scientific data, software and papers. This work aims tackling the needs for a fine-grained description of multidisciplinary scientific collaborations, from data creation to cross-fertilization. A framework for hosting comprehensive and semantic metadata for multidisciplinary scientific teams is proposed. The platform provides a user-friendly online interface for data description, browsing and access. This research has been conducted in collaboration with the multidisciplinary dataNooS academic alliance. CALLISTO is developed and maintained at the computing centre CALMIP

CALLISTO: a Semantics-Based Platform for Sharing FAIR Scientific Data

International audienceIn this paper, the platform CALLISTO (CALmip Launches an Interface for a Semantic Toolbox Online, https://callisto.calmip.univ-toulouse.fr/) is presented, aiming at open science construction around semantic description of scientific data, software and papers. This work aims tackling the needs for a fine-grained description of multidisciplinary scientific collaborations, from data creation to cross-fertilization. A framework for hosting comprehensive and semantic metadata for multidisciplinary scientific teams is proposed. The platform provides a user-friendly online interface for data description, browsing and access. This research has been conducted in collaboration with the multidisciplinary dataNooS academic alliance. CALLISTO is developed and maintained at the computing centre CALMIP

CALLISTO: a Semantics-Based Platform for Sharing FAIR Scientific Data

International audienceIn this paper, the platform CALLISTO (CALmip Launches an Interface for a Semantic Toolbox Online, https://callisto.calmip.univ-toulouse.fr/) is presented, aiming at open science construction around semantic description of scientific data, software and papers. This work aims tackling the needs for a fine-grained description of multidisciplinary scientific collaborations, from data creation to cross-fertilization. A framework for hosting comprehensive and semantic metadata for multidisciplinary scientific teams is proposed. The platform provides a user-friendly online interface for data description, browsing and access. This research has been conducted in collaboration with the multidisciplinary dataNooS academic alliance. CALLISTO is developed and maintained at the computing centre CALMIP