AnnotQTL

Welcome to AnnotQTL

AnnotQTL

The AnnotQTL server is a tool designed to gather the functional annotation of genes from several institutional databases for a specific chromosomal region. This tool was initially designed to help the characterization of the genes in a QTL interval region in order to select the best candidate genes. Therefore, it provides the location of the genes in a specific region (using the NCBI and Ensembl data) and adds the functional annotation available from others databases (Gene Ontology - GO, Mammalian Phenotype - MP, HGNC, Pubmed, etc).

With the GO and MP data, we introduce a “highlight” feature for the genes annotated with a specific GO term or MP term. Indeed, it is most relevant to highlight some genes annotated with a specific term (i.e. a term that may be biologically relevant for your studied phenotype).

Several information of comparative mapping of the selected species with the Human genome are provided (using a local dump of the data provided by the Narcisse website); orthologous genes from the Human and mouse genome (Ensembl database) can be used optionnaly.

Finally, custom marker list can be included in the result display to select the genes that are the closest from your most significant markers. This feature works with all types of markers (i.e. microsatellites, snp, ...) as long as a genomic location in bases is provided by the user.

If your species of interest is not present in the species list, feel free to contact us using this form.

If you use AnnotQTL, please cite:

AnnotQTL: a new tool to gather functional and comparative information on a genomic region F. Lecerf; A. Bretaudeau; O. Sallou; C. Desert; Y. Blum; S. Lagarrigue; O. Demeure Nucleic Acids Research 2011; doi: 10.1093/nar/gkr361

News:

09.07.2011: Human and mouse genome are now represented in AnnotQTL. Please note that this functionality is available for development and beta testing.

06.06.2011: a SOAP webservice is now available (see the tutorial). You can now also use STS or SNP ids to define chromosomal locations on the request page.

04.14.2011: a batch request option has been added to AnnotQTL. Now, you can run multiple analyses of several QTL regions.

01.27.2011: the mouse genome has been added to the genomic synteny conservation comparison in AnnotQTL! Now, you can select "Mus musculus" in the synteny conservation options to compare your genomic region of interest to the mouse one.

Click on the above button to try out AnnotQTL for a request in the Gallus gallus genome, chromosome 5:55000000..60000000, with the following options:

  • highlight in yellow with GO id GO:0006629 (adding GOA from Mmu and Hsa),
  • highlight in pink with Mammalian Phenotype using keyword "adip" and querying all fields,
  • add the synteny conservation information with the Human genome (synt order = 3) and completing these data with Ensembl data.

Actual statistics:

Database Version
Ensembl v. 73
NCBI annotation June 2012
OMIM, GO, MP, snp June 2012
Narcisse January 2011
Genome assembly Version
Bos taurus Btau_4.2
Gallus gallus Gallus_gallus-2.1
Canis lupus familiaris Dog2.0
Equus caballus EquCab2
Sus scrofa Sscrofa9.2
Homo sapiens GRCh37.p2
Mus musculus MGSCv37
Rattus Norvegicus RGSC_v3.4
Danio Rerio Zv9

INRA Agrocampus Ouest Biogenouest IRISA INRIA Université de Rennes 1 Région Bretagne

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