Service list
Name of service | Description | Related links* |
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ANISEED |
ANISEED is the main model organism database for the worldwide community of scientists working on a class of marine invertebrates, the tunicates (sister-group of vertebrates). It integrates for each species: a main knowledge base with extended information on gene function, gene expression, phylogeny and embryonic anatomy at single cell resolution; a genomic browser and a Genomicus gene synteny browser. |
bio.toolsFAIRsharing |
CRISPRCas++ |
CRISPRCas++ is a new website holding a program called CRISPRCasFinder to detect CRISPR arrays and cas genes in the genome of prokaryotes. CRISPRCasMeta is adapted to the analysis of large metagenomic data. The programs are available online or can be downloaded for local usage. A database called CRISPRCasdb, the successor of CRISPRdb, is accessible on the CRISPRCas++ website. It can be browsed and queried in search for repeat and spacer sequences. |
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FAIDARE |
FAIDARE is a portal developed by ELIXIR-FR as an asset of the ELIXIR Plant Science community. FAIDARE enables data discovery through federations of distant Plant informations systems that have set up a standardized Restful API, the BrAPI. FAIDARE currently allows to do detailed searches of accessions and phenotyping data. |
bio.tools |
GenomeHubs |
The South Green Genome Hub is a suite of crop-specific community portals to manage genomic datasets with focus on tropical and Mediterranean plants. Currently developed on Banana, Cassava, Cacao, Coffee, Grass, Rice and Sugarcane, genome hubs provide access to multiple datasets (e.g. assemblies, gene product information, metabolic pathways, gene families, transcriptomics and genetic markers). |
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GENOMICUS |
Genomicus is a database and a web server that integrates comparative genome data and ancestral genome reconstruction in a fast and intuitive way. It enables users to navigate in genomes in several dimensions: linearly along chromosome axes, transversaly across different species, and chronologicaly along evolutionary time. A user-friendly graphical interface allows syntenic comparisons and gene order alignments between pairs of genomes or multiple genomes at different scales: local gene order, karyotypes, matrix plots, etc. Different phylums such as Vertebrates, Plants, Fungi, Metazoa (as per Ensembl Genomes) are represented and regularly updated, as well as specific versions on Tunicates, Fish and Amphioxus. |
bio.tools |
GnpIS |
GnpIS is an interoperable Information System for plant and pest genomics. It is a powerful multispecies centralized information system with seven linked relational databases. |
bio.toolsFAIRsharing |
IMGT |
An integrated knowledge resource specialized in the immunoglobulins (IG) or antibodies, T cell receptors (TR), and major histocompatibility (MH) of human and other vertebrate species. |
bio.toolsFAIRsharing |
LoRDEC |
LoRDEC is a standalone software for error correcting long reads (from Pacific Biosciences, or Oxford Nanopore) with a hybrid approach. LoRDEC uses short reads to correct long reads; it combines sequencing data from both the second and third generation technologies. It can be easily integrated in any pipeline for processing deep sequencing data. LoRDEC's originality is to build a graph that summarize all short reads, and then to align the long reads against this graph to correct them. This makes LoRDEC a very efficient tool to process large datasets. It has been widely used in whole genome or transcriptome projects around the world. |
bio.tools |
MetExplore |
MetExplore is a free and open webserver for the analysis of omics data in the context of genome scale metabolic networks. MetExplore allows the collaborative curation of metabolic networks. In the specific case of metabolomics, it provides mining algorithms such as MetaboRank, a recommendation system for enhanced metabolic fingerprinting. Overall, Metexplore orginality relies in its ability to allow taylor made metabolic network visualisation using an open source javascript library: MetExploreViz. |
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MicroScope |
MicroScope is an integrated Web platform for the annotation and exploration of microbial gene functions through genomic, pangenomic and metabolic comparative analysis. It supports submissions of newly assembled genomes and metagenomes, and also provides analysis services for RNA-seq data. The user interface of MicroScope enables collaborative work in a rich comparative context to improve community-based curation efforts. |
bio.toolsFAIRsharingTeSS |
Ocean Gene Atlas |
The Ocean Gene Atlas service provides data mining access to three complementary data objects: gene sequence catalogs (ENA), sample environmental context (PANGAEA), and gene abundances estimates in samples (computed by mapping raw sequence reads onto gene catalogs). User queries are composed of either a sequence (nucleic or protein), or a hidden Markov model derived from a multiple sequence alignment. Homologs of the user query in the gene catalogs are identified using standard sequence similarity search tools (eg BLAST or HMMER), and their read based estimated abundance are displayed in interactive world maps and ecological plots. A phylogenetic tree is also inferred in order to situate the user query within its context of marine environmental homologs as well as known homologs from reference sequences. |
bio.tools |
Orphadata |
Orphadata provides the scientific community with comprehensive, quality data sets related to rare diseases and orphan drugs from the Orphanet knowledge base, in reusable formats. |
bio.toolsFAIRsharing |
Orphanet |
Orphanet is the reference resource for information and data on rare diseases and orphan drugs. Orphanet derives from its knowledge base an ontology of rare diseases, information on rare diseases and data on rare diseases. |
bio.toolsFAIRsharing |
ParameciumDB |
ParameciumDB is a community model organism database for the ciliate Paramecium. The web site gives access to genomes of many Paramecium species and their annotations. ParameciumDB also integrates genome-wide datasets (DNA-seq, RNA-seq, ChIP-seq) provided by the community. This portal is used to query, retrieve, visualize and compare the most up-to-date public data. |
bio.tools |
PhyML |
PhyML is a software that estimates maximum likelihood phylogenies from alignments of nucleotide or amino acid sequences. The main strength of PhyML lies in the large number of substitution models coupled to various options to search the space of phylogenetic tree topologies, going from very fast and efficient methods to slower but generally more accurate approaches. PhyML was designed to process moderate to large data sets. In theory, alignments with up to 4,000 sequences 2,000,000 character-long can be processed. PhyML can process data sets made of multiple genes and fit sophisticated substitution models with heterogeneous components across partition elements. |
bio.tools |
REPET |
The REPET package integrates bioinformatics pipelines dedicated to detecte, annotate and analyse transposable elements (TEs) in genomic sequences. The main pipelines are (i) TEdenovo, which search for interspersed repeats, build consensus sequences and classify them according to TE features, and (ii) TEannot, which mines a genome with a library of TE sequences, for instance the one produced by the TEdenovo pipeline, to provide TE annotations exported into GFF3 files. |
bio.tools |
VarAFT |
VarAFT is a software designed to annotate and filter Human NGS data. This system was developed within the RD-Connect project and was instrumental for the creation of the RD-Connect Genome-Phenome platform. As a stand-alone java system, it ensures full data protection, critical for clinical use. VarAFT provides experiments’ quality, annotates, and allows the filtration of VCF files. Data from multiple samples can be combined to address different Mendelian Inherited Disorders, Population Genetics or Cancers. It contains unique variant priorization features including OMIM, HPO, Gene Ontology, pathways and predictions from UMD-Predictor and Human Splicing Finder in addition to classical annotations from dbNSFP . It is used by many research and clinical laboratories worldwide. |
bio.tools |
WheatIS |
WheatIS is a portal that enables data discovery through an international federation of distant informations systems about wheat genetics and genomics in the frame of the Wheat Initiative (www.wheatinitiative.org). The WheatIS portal allows a keyword-based discovery of any type of data. It currently gives a single entry point to data provided by twelve different worldwide institutes. |
bio.tools |