QGene 4.0, an extensible Java QTL-analysis platform

Bioinformatics

Volumn 24, Issue 23, 2008, Pages 2788-2789

  Joehanes, Roby ^a   Nelson, James C ^a  

^a KANSAS STATE UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; COMPUTER AIDED DESIGN; COMPUTER INTERFACE; DATA ANALYSIS SOFTWARE; GENE MAPPING; GENOTYPE; PRIORITY JOURNAL; QUANTITATIVE TRAIT LOCUS; SIMULATOR; STATISTICAL ANALYSIS;

COMPUTATIONAL BIOLOGY; CROSSES, GENETIC; INBREEDING; PROGRAMMING LANGUAGES; QUANTITATIVE TRAIT LOCI; SOFTWARE;

EID: 56649122104     PISSN: 13674803     EISSN: 14602059     Source Type: Journal    
DOI: 10.1093/bioinformatics/btn523     Document Type: Article

References (27)

1. Broman,K.W. et al. (2003) R/qtl: QTL mapping in experimental crosses. Bioinformatics, 19, 889-890.
2. Churchill,G.A. and Doerge,R.W. (1994) Empirical threshold values for quantitative trait mapping. Genetics, 138, 963-971.
3. Haley,C.S. and Knott,S.A. (1992) A simple regression method for mapping quantitative trait loci in line crosses using flanking markers. Heredity, 69, 315-324.
4. Jansen,R.C. (1993) Interval mapping of multiple quantitative trait loci. Genetics, 135, 205-211.
5. Jiang,C. and Zeng,Z.-B. (1995) Multiple trait analysis of genetic mapping for quantitative trait loci. Genetics, 140, 1111-1127.
6. Jiang,C. and Zeng,Z.-B. (1997) Mapping quantitative trait loci with dominant and missing markers in various crosses from two inbred lines. Genetica, 101, 47-58.
7. Jourjon,M.-F. et al. (2004) MCQTL: Multi-allelic QTL mapping in multi-cross design. Bioinformatics, 21, 128-130.
8. Kao,C.-H. et al. (1999) Multiple interval mapping for quantitative trait loci. Genetics 152, 1203-1216.
9. Korol,A.B. et al. (1995) Interval mapping of quantitative trait loci employing correlated trait complexes. Genetics, 140, 1137-1147.
10. Kumar,S. et al. (2008) MEGA: A biologist-centric software for evolutionary analysis of DNA and protein sequences. Brief. Bioinform. 9, 299-306.
11. Lander,E.S. and Botstein,D. (1989) Mapping Mendelian factors underlying quantitative traits using RFLP linkage maps. Genetics, 121, 185-199.
12. Manly,K.F. and Olson,J.M. (1999) Overview of QTL mapping software and introduction to Map Manager QT. Mamm. Genome, 10, 327-334.
13. Nelson,J.C. (1997) QGENE: Software for marker-based genomic analysis and breeding. Mol. Breed., 3, 239-245.
14. Satagopan,J.M. et al. (1996) A Bayesian approach to detect quantitative trait loci using Markov chain Monte Carlo. Genetics, 144, 805-816.
15. Seaton,G. et al. (2002) QTL express: Mapping quantitative trait loci in simple and complex pedigrees. Bioinformatics, 18, 339-340.
16. Seaton,G. et al. (2006) GridQTL: A grid portal for QTL mapping of compute intensive datasets. In Proceedings of the 8th World Congress on Genetics Applied to Livestock Production. Belo Horizonte, Brazil.
17. Sen,S. and Churchill,G.A. (2001) A statistical framework for quantitative trait mapping. Genetics, 159, 371-387.
18. Shannon,P. et al. (2003) Cytoscape: A software environment for integrated models of biomolecular interaction networks. Genome Res. 13, 2498-2504.
19. Sillanpää,M.J. and Arjas,E. (1998) Bayesian mapping of multiple quantitative trait loci from incomplete inbred line cross data. Genetics, 148, 1373-1388.
20. Wang,D.L. et al. (1999) Mapping QTLs with epistatic effects and QTL x environment interactions by mixed linear model approaches. Theor. Appl. Genet., 99, 1255-1264.
21. Wang,S. et al. (2007) Windows QTL Cartographer 2.5. Department of Statistics, North Carolina State University, Raleigh, NC. Available at http://statgen.ncsu.edu/qtlcart/WQTLCart.htm. Last accessed date 20th October 2008.
22. Wu,H. et al. (2008) J/qtl, Java GUI for the popular QTL data analysis software R/qtl. Available at http://research.jax.org/faculty/ churchill/software/Jqtl/index.html. Last accessed date 20th October 2008.
23. Xu,S. (2003) Estimating polygenic effects using markers of the entire genome. Genetics, 163, 789-801.
24. Xu,S. and Atchley,W.R. (1995) A random model approach to interval mapping of quantitative trait loci. Genetics, 141, 1189-1197.
25. Yang,J. et al. (2008) QTLNetwork: Mapping and visualizing genetic architecture of complex traits in experimental populations. Bioinformatics, 24, 721-723.
26. Zeng,Z.-B. (1994) Precision mapping of quantitative trait loci. Genetics, 136, 1457-1468.
27. Zhang,Y.-M. and Xu,S. (2005)Apenalized maximum likelihood method for estimating epistatic effects of QTL. Heredity, 95, 96-104.