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. 2007 Jan;35(Database issue):D604-9.
doi: 10.1093/nar/gkl946. Epub 2006 Nov 29.

AnimalQTLdb: a livestock QTL database tool set for positional QTL information mining and beyond

Zhi-Liang Hu  1 , Eric Ryan Fritz, James M Reecy
Affiliations

AnimalQTLdb: a livestock QTL database tool set for positional QTL information mining and beyond

Zhi-Liang Hu et al. Nucleic Acids Res. 2007 Jan.

Abstract

The Animal Quantitative Trait Loci (QTL) database (AnimalQTLdb) is designed to house all publicly available QTL data on livestock animal species from which researchers can easily locate and compare QTL within species. The database tools are also added to link the QTL data to other types of genomic information, such as radiation hybrid (RH) maps, finger printed contig (FPC) physical maps, linkage maps and comparative maps to the human genome, etc. Currently, this database contains data on 1287 pig, 630 cattle and 657 chicken QTL, which are dynamically linked to respective RH, FPC and human comparative maps. We plan to apply the tool to other animal species, and add more structural genome information for alignment, in an attempt to aid comparative structural genome studies (http://www.animalgenome.org/QTLdb/).

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Figures

Figure 1
Figure 1
Popup menus and forms (in red circles) were added in the QTLdb ‘chromosome view’ to link from a QTL region to the RH-human comparative maps or FPC clone maps.
Figure 2
Figure 2
The linked RH-human map showing the region of human chromosome 2, which corresponds to pig chromosome 3 that harbors a QTL for pig basal glucose levels (BGL). Note the interested QTL region is highlighted.
Figure 3
Figure 3
A snap shot of Linkage-FPC map alignment on SSC 8 based on blast information.
Figure 4
Figure 4
Data flow and curator/editor/administrator work flow built into the QTLdb curator/editor tools.
Figure 5
Figure 5
Schematic view of the QTLdb that are designed to enable dynamic links to external data resources (Dotted links: work is on the way to make links; Gray box/lines: data type is planned but does not have actual data yet; Single line boxes: data types; Double line boxes: Databases).
See this image and copyright information in PMC

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