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"description": "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 sequence reads onto gene catalogs).\nUser 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 maps and 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.",
"homepage": "http://tara-oceans.mio.osupytheas.fr/ocean-gene-atlas/",
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],
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],
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"http://edamontology.org/topic_3387",
"http://edamontology.org/topic_3174",
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],
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"name": "MIO",
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},
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"name": "OCEANOMICS",
"email": null,
"url": "http://www.oceanomics.eu/",
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"typeEntity": "Funding agency",
"note": "ANR-11-BTBR-0008"
},
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"url": "http://tara-oceans.mio.osupytheas.fr/ocean-gene-atlas/credits",
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"maturity": "Mature",
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"last_update": "2024-11-24T20:59:34.208631Z",
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},
{
"id": 173,
"name": "Tango",
"description": "A computer algorithm for prediction of aggregating regions in unfolded polypeptide chains. The model used here, is designed to predict cross-beta aggregation in peptides and denatured proteins and consists of a phase-space encompassing the random coil and 4 possible structural states: beta-turn, alpha-helix, beta-sheet aggregation and alpha-helical aggregation.",
"homepage": "http://tango.crg.es/",
"biotoolsID": "tango",
"biotoolsCURIE": "biotools:tango",
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],
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"scientific_topics": [
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"http://edamontology.org/topic_3510",
"http://edamontology.org/topic_0081"
],
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"Linux",
"Windows"
],
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],
"name": null,
"email": null,
"url": "http://tango.crg.es/support.jsp",
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"note": null
}
],
"tool_licence": null,
"documentation": "http://tango.crg.es/Tango_Handbook.pdf",
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"cost": null,
"unique_visits": 0,
"citations": null,
"annual_visits": 0,
"last_update": "2018-12-10T12:58:45Z",
"teams": [
"CBiB"
],
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},
{
"id": 157,
"name": "OCG",
"description": "Creates an overlapping class system from an unweighted simple graph G = (V,E).OCG is essentially a hierarchical ascending algorithm. By default, it will fuse the initial classes until further fusions do not increase the modularity but other options are available.",
"homepage": "http://tagc.univ-mrs.fr/tagc/index.php/software/17",
"biotoolsID": "ocg",
"biotoolsCURIE": "biotools:ocg",
"tool_type": [
"Command-line tool"
],
"collection": [],
"scientific_topics": [
"http://edamontology.org/topic_0128",
"http://edamontology.org/topic_0602",
"http://edamontology.org/topic_1775"
],
"primary_publication": [],
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"Linux",
"Windows",
"Mac"
],
"tool_credit": [
{
"type_role": [
"Primary contact"
],
"name": "Brun C",
"email": "brun@tagc.univ-mrs.fr",
"url": "http://tagc.univ-mrs.fr/tagc/",
"orcidid": null,
"gridid": null,
"typeEntity": "Person",
"note": null
}
],
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"citations": null,
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"last_update": "2024-11-25T16:02:04.280293Z",
"teams": [
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],
"source_repository": null
},
{
"id": 245,
"name": "Gbrowse giant virus",
"description": "A genome browser instance dedicated to giant viruses discovered by the IGS Laboratory",
"homepage": "https://www.igs.cnrs-mrs.fr/cgi-bin/gb2/gbrowse",
"biotoolsID": "gbrowse_giant_virus",
"biotoolsCURIE": "biotools:gbrowse_giant_virus",
"tool_type": [],
"collection": [],
"scientific_topics": [],
"primary_publication": [],
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"tool_credit": [],
"tool_licence": null,
"documentation": null,
"maturity": null,
"cost": null,
"unique_visits": null,
"citations": null,
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"last_update": "2022-12-01T20:12:00.006926Z",
"teams": [],
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},
{
"id": 239,
"name": "ACDtool",
"description": "Web-server for the generic analysis of large data sets of counts.",
"homepage": "https://www.igs.cnrs-mrs.fr/acdtool/",
"biotoolsID": "acdtool",
"biotoolsCURIE": "biotools:acdtool",
"tool_type": [
"Web application"
],
"collection": [],
"scientific_topics": [
"http://edamontology.org/topic_2269"
],
"primary_publication": [],
"operating_system": [],
"tool_credit": [],
"tool_licence": null,
"documentation": null,
"maturity": null,
"cost": "Free of charge",
"unique_visits": null,
"citations": null,
"annual_visits": null,
"last_update": "2025-12-10T09:25:24.490675Z",
"teams": [
"PACA-Bioinfo"
],
"source_repository": null
},
{
"id": 101,
"name": "Genomicus-plants",
"description": "Genomicus-Plants is a genome browser that enables users to navigate in plants genomes in several dimensions: linearly along chromosome axes, transversaly across different species, and chronologicaly along evolutionary time.",
"homepage": "https://www.genomicus.biologie.ens.fr/genomicus-plants",
"biotoolsID": "Genomicus-Plants",
"biotoolsCURIE": "biotools:Genomicus-Plants",
"tool_type": [
"Database portal",
"Web application"
],
"collection": [
"elixir-fr-sdp-2019",
"GENOMICUS"
],
"scientific_topics": [
"http://edamontology.org/topic_3943",
"http://edamontology.org/topic_3299",
"http://edamontology.org/topic_0621",
"http://edamontology.org/topic_0797",
"http://edamontology.org/topic_0622",
"http://edamontology.org/topic_0623",
"http://edamontology.org/topic_0780"
],
"primary_publication": [
"10.1093/nar/gks1156",
"10.1093/pcp/pcu177"
],
"operating_system": [],
"tool_credit": [
{
"type_role": [
"Support"
],
"name": null,
"email": "genomicus-web@ens.fr",
"url": null,
"orcidid": null,
"gridid": null,
"typeEntity": null,
"note": null
},
{
"type_role": [
"Primary contact"
],
"name": "Hugues Roest Crollius",
"email": "hrc@ens.fr",
"url": "http://www.ibens.ens.fr/?rubrique43",
"orcidid": "http://orcid.org/0000-0002-8209-173X",
"gridid": null,
"typeEntity": "Person",
"note": null
},
{
"type_role": [
"Primary contact"
],
"name": "Alexandra Louis",
"email": "alouis@biologie.ens.fr",
"url": "http://www.ibens.ens.fr/spip.php?article182",
"orcidid": "http://orcid.org/0000-0001-7032-5650",
"gridid": null,
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}
],
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"maturity": "Mature",
"cost": "Free of charge",
"unique_visits": null,
"citations": null,
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"last_update": "2020-06-16T10:55:27Z",
"teams": [
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],
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},
{
"id": 279,
"name": "FINSURF",
"description": "FINSURF (Functional Identification of Non-coding Sequences Using Random Forests) is a tool designed to analyse lists of sequences variants in the human genome.\nIt assigns a score to each variant, reflecting its functional importance and therefore its likelihood to disrupt the physiology of its carrier. FINSURF scores Single Nucleotide Variants (SNV), insertions and deletions. Among SNVs, transitions and transversions are treated separately. Insertions are characterised by a score given to each base flanking the insertion point. Deletions are characterised by a score at every deleted base. FINSURF can (optionally) use a list of known or suspected disease genes, in order to restrict results to variants overlapping cis-regulatory elements linked to these genes.\n\nFor a variant of interest, users can generate a graphical representation of \"feature contributions », showing the relative contributions of genomic, functional or evolutionary information to its score.",
"homepage": "https://www.finsurf.bio.ens.psl.eu/",
"biotoolsID": "finsurf",
"biotoolsCURIE": "biotools:finsurf",
"tool_type": [
"Web application",
"Command-line tool"
],
"collection": [],
"scientific_topics": [
"http://edamontology.org/topic_0749",
"http://edamontology.org/topic_0634",
"http://edamontology.org/topic_3673",
"http://edamontology.org/topic_3577",
"http://edamontology.org/topic_3300"
],
"primary_publication": [
"10.1371/journal.pgen.1010191"
],
"operating_system": [
"Mac",
"Linux"
],
"tool_credit": [
{
"type_role": [
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],
"name": null,
"email": "finsurf@bio.ens.psl.eu",
"url": null,
"orcidid": null,
"gridid": null,
"typeEntity": null,
"note": null
},
{
"type_role": [],
"name": "IBENS - DYOGEN Team",
"email": null,
"url": null,
"orcidid": null,
"gridid": null,
"typeEntity": "Institute",
"note": null
},
{
"type_role": [
"Primary contact"
],
"name": "Hugues Roest Crollius",
"email": "hrc@bio.ens.psl.eu",
"url": null,
"orcidid": "http://orcid.org/0000-0002-8209-173X",
"gridid": null,
"typeEntity": "Person",
"note": null
},
{
"type_role": [
"Developer"
],
"name": "Lambert Moyon",
"email": "moyon@bio.ens.psl.eu",
"url": null,
"orcidid": "https://orcid.org/0000-0003-2390-3942",
"gridid": null,
"typeEntity": "Person",
"note": null
},
{
"type_role": [
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],
"name": "Alexandra Louis",
"email": "alexandra.louis@bio.ens.psl.eu",
"url": null,
"orcidid": "https://orcid.org/0000-0001-7032-5650",
"gridid": null,
"typeEntity": "Person",
"note": null
},
{
"type_role": [
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],
"name": "Camille Berthelot",
"email": null,
"url": null,
"orcidid": "https://orcid.org/0000-0001-5054-2690",
"gridid": null,
"typeEntity": "Person",
"note": null
}
],
"tool_licence": null,
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"maturity": null,
"cost": "Free of charge",
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"citations": null,
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"last_update": "2024-11-24T14:55:59.341655Z",
"teams": [
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],
"source_repository": "https://github.com/DyogenIBENS/FINSURF/"
}
]
}