OrthoInspector statistics

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Associated diseases

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OrthoInspector specifications

Information


Unique identifier OMICS_05344
Name OrthoInspector
Software type Toolkit/Suite
Interface Command line interface, Graphical user interface, Application programming interface
Restrictions to use None
Input format Fasta
Output data A SQL database and text files.
Operating system Unix/Linux, Mac OS, Windows
Programming languages Java
Database management system MySQL, Oracle, PostgreSQL, SQLite
License GNU General Public License version 3.0
Computer skills Advanced
Version 3.0
Stability Stable
Maintained Yes

Versioning


Add your version

Maintainer


  • person_outline Odile Lecompte <>

Additional information


Previous version: http://www.lbgi.fr/orthoinspector/ Tutorial: http://lbgi.fr/orthoinspectorv3/tutorials

Publications for OrthoInspector

OrthoInspector in pipeline

2013
PMCID: 3726750
PMID: 23922843
DOI: 10.1371/journal.pone.0069890

[…] in arabidopsis thaliana, and screened for homology in the other five plant species (brachypodium distachyon, oryza sativa, populus trichocarpa, vitis vinifera, and zea mays), using the blast tool, orthoinspector, tair, rice genome annotation project information. if one gene could not be identified in any other species, the arabidopsis gene model was dropped, and the next contiguous gene […]


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OrthoInspector in publications

 (5)
PMCID: 5850483
PMID: 28460059
DOI: 10.1093/molbev/msx146

[…] cycle of these species is only partially deciphered. these six species will be referred to as “potentially ciliated species” in the following sections. orthology relationships were predicted using orthoinspector () and the presence/absence of orthologs recorded in a binary matrix where rows represent genes and columns represent species. to exploit the phylogenetic profiles and discriminate […]

PMCID: 4852459
PMID: 27248802
DOI: 10.1098/rsob.160009

[…] pre-grcz10 paths, the latest grcz10 gene set (ensembl80) might differ marginally from the described results., we used the zebrafish gene identifiers for the conserved nlrs in zebrafish to query the orthoinspector v. 2.0 database [] at http://lbgi.igbmc.fr/orthoinspector for orthologues in published genomes and downloaded the corresponding sequence. we then queried a custom blast database […]

PMCID: 4827703
PMID: 27043882
DOI: 10.1038/nmeth.3830

[…] compara, panther 8.0, and phylomedb. seven are graph-based (i.e. based on pairwise comparisons): best reciprocal hits (brh), reciprocal smallest distance (rsd), eggnog, hieranoid, inparanoid, oma, orthoinspector. finally, metaphors is a meta-method incorporating both tree-based and graph-based methods. for some of the methods, multiple variants are included in the analysis. details […]

PMCID: 3726750
PMID: 23922843
DOI: 10.1371/journal.pone.0069890

[…] –. the homologous gene annotation files for plants were downloaded from genoscope (http://www.genoscope.cns.fr/externe/genomebrowser/vitis/), tair (http://www.arabidopsis.org/), orthoinspector (http://lbgi.igbmc.fr/orthoinspector/), and rice genome annotation project database (http://rice.plantbiology.msu.edu/) , , . the 16s rrna sequence dataset was downloaded […]

PMCID: 3526444
PMID: 23281701
DOI: 10.1186/1471-2105-13-S19-S16

[…] been conceived with inparalog detection specifically in mind. to our knowledge, the only methods that explicitly consider inparalog detection are inparanoid [], multiparanoid [], orthomcl [], and orthoinspector [], all of which employ the same basic methodology for inparalog detection: the best similarity between genes in different genomes is evidence for orthology, inparalogs […]


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OrthoInspector institution(s)
Department of Computer Science, ICube, UMR 7357, University of Strasbourg, CNRS, Federation de Medecine Translationnelle de Strasbourg, Strasbourg, France; LIRMM, Univ Montpellier, CNRS, Montpellier, France; ISEM, Univ Montpellier, CNRS, IRD, EPHE, CIRAD, INRAP, Montpellier, France; AGAP, Univ Montpellier, CIRAD, INRA, Montpellier Supagro, Montpellier, France
OrthoInspector funding source(s)
Supported by Agence Nationale de la Recherche [BIPBIP: ANR-10- BINF-03–02, ReNaBi-IFB: ANR-11-INBS-0013, Labex Agro: ANR-10-LABX-0001–01 to B.L., Labex CeMEB: ANR-10-LABX-0004, Labex NUMEV: ANR-10- LABX-20]; Institute funds from the Centre National de la Recherche Scientifique and the Universite de Strasbourg.

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