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chevron_left Functional annotation Gene Ontology annotation Annotation workflows QTL mapping chevron_right
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AnnotQTL specifications

Information


Unique identifier OMICS_23292
Name AnnotQTL
Software type Application/Script
Interface Web user interface
Restrictions to use None
Programming languages Perl
Database management system MySQL
Computer skills Basic
Stability Stable
Maintained Yes

Maintainer


  • person_outline Frederic Lecerf <>

Publication for AnnotQTL

AnnotQTL in publications

 (5)
PMCID: 4534097
PMID: 26267269
DOI: 10.1371/journal.pone.0135488

[…] it is significant, 4 qtl effect as a proportion of the phenotypic standard deviation of trait, 5 ns: p>0.150 at the genome wide level, 6 number of genes in the qtl region, as found by http://annotqtl.genouest.org/ interrogation, several of these qtls co-localized with qtls for other traits detected in the same experiment. first, co-localizations were found with the anatomy of the gut, […]

PMCID: 4205046
PMID: 25333370
DOI: 10.1371/journal.pone.0111299

[…] we removed genotypes for which the global depth dp (depth) was under 3 or higher than 60 (mean depth + 6σ), using vcftools ., to identify positional candidate genes in highlighted qtl regions, annotqtl software was used, providing the location of genes in a specific region using ncbi and ensembl databases, and filtering them onto ontology annotation criterion. thus, genes belonging […]

PMCID: 3936936
PMID: 24552175
DOI: 10.1186/1297-9686-46-14

[…] limits were determined on the basis of the chicken linkage consensus map constructed by groenen et al. [], as described previously. the list of genes present in each qtl region was extracted using annotqtl [] on the wugsc 2.1 (galgal3) assembly. the functions and interactions of these genes were analyzed using ingenuity pathway analysis (ipa, http://www.ingenuity.com)., the 860 f2 animals […]

PMCID: 3851061
PMID: 24079476
DOI: 10.1186/1297-9686-45-36

[…] qtl were identified in this study, with intervals that contain for most of them a few dozen genes. from among these positional candidate genes, functional candidate genes were identified using the annotqtl web tool [] for qtl regions that were significant at the genome level (p < 0.05). for bmwmin on gga2 and tb on gga5, none of the described genes had a function that could be linked […]

PMCID: 3428659
PMID: 22613937
DOI: 10.1186/1471-2164-13-198

[…] qtls (95 %) were calculated by using the one-lod drop-off method following lander and botstein []., for all qtls detected using the one-qtl analysis, candidate genes were identified by the software annotqtl [], available at http://annotqtl.genouest.org. this tool was designed to assist the characterization of genes in a qtl region as a step towards selecting the best candidate genes. […]


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AnnotQTL institution(s)
INRA, UMR598 Génétique Animale, Rennes, France; Agrocampus OUEST, UMR598 Génétique Animale, Rennes, France; GenOuest Platform, INRIA/Irisa – Campus de Beaulieu, Rennes, France; Agrocampus OUEST, Applied Mathematics Department, Rennes, France
AnnotQTL funding source(s)
Supported by INRA, Agrocampus Ouest, the Regional Council of Brittany; French Ministry in charge of Agriculture (DGER).

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