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Mammalian Genome

, Volume 18, Issue 1, pp 1–4 | Cite as

Animal QTLdb: beyond a repository

A public platform for QTL comparisons and integration with diverse types of structural genomic information
  • Zhi-Liang Hu
  • James M. Reecy
Informatics

Abstract

Over the past ten years there have been a large number of publications that have described hundreds of quantitative trait loci (QTL) in livestock species. To facilitate the comparison of QTL results across experiments, the Animal QTL database (QTLdb) was developed to house all published QTL information as a public repository. The QTLdb was originally developed to serve the porcine genomics community (previously known as PigQTLdb). We have further developed the QTLdb to house QTL data from multiple species, including but not limited to cattle, chickens, and pigs. In addition, tools have been developed to allow QTL map alignments against consensus linkage maps, radiation hybrid (RH) maps, BAC fingerprinted contig (FPC) maps, single nucleotide polymorphism (SNP) location maps, and human maps. In addition, we have expanded the capabilities of the database such that research tools were developed where “private” preliminary QTL data could be entered and compared against all public data. This allows researchers to visualize data before publication and compare it with published results to aid in data interpretation. To serve this purpose, the database curator/editor tools also include functions that allow registered users to enter their own QTL data, make use of the QTLdb tools for data analysis, and use the QTLdb as a publishing tool (URL: http://www.animalgenome.org).

Keywords

Quantitative Trait Locus Radiation Hybrid Single Nucleotide Polymorphism Location Quantitative Trait Locus Data Quantitative Trait Locus Information 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.

Notes

Acknowledgment

The authors express their appreciation to Stacey Meyers, Jonathan Beever, Denis Larkin, and Harris Lewin from the University of Illinois; Sean Humphray, Carol Scott, and Jane Rogers from Sanger Institute; Max Rothschild, Behnam Abasht, and Susan Lamont from Iowa State University; and Martien Groenen from Wageningen University for various data and their generous help. They have greatly accelerated progress on this project. The authors are also in debt to Eric Ryan Fritz for his diligent effort as a data curator.

References

  1. Fadiel A, Anidi I, Eichenbaum KD (2005) Farm animal genomics and informatics: an update. Nucleic Acids Res 33(19), 6308–6318PubMedCrossRefGoogle Scholar
  2. Hu ZL, Fritz ER, Reecy JM (2006) AnimalQTLdb: a livestock QTL database tool set for positional QTL information mining and beyond. Nucleic Acids Res Epub. NAR Dec 13 2006. doi: 10.1093/nar/gKL946Google Scholar
  3. Hu ZL, Dracheva S, Jang W, Maglott D, Bastiaansen J, et al. (2005) A QTL resource and comparison tool for pigs: PigQTLDB. Mamm Genome 16(10), 792-800PubMedCrossRefGoogle Scholar
  4. Korstanje R, Paigen B (2002) From QTL to gene: The harvest begins. Nat Genet 31, 235–236PubMedCrossRefGoogle Scholar

Copyright information

© Springer Science+Business Media, Inc. 2007

Authors and Affiliations

  • Zhi-Liang Hu
    • 1
  • James M. Reecy
    • 1
  1. 1.Department of Animal ScienceCenter for Integrated Animal Genomics, Iowa State UniversityAmesUSA

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