Lep-MAP: Fast and accurate linkage map construction for large SNP datasets

Bioinformatics

Volumn 29, Issue 24, 2013, Pages 3128-3134

  Rastas, Pasi ^a   Paulin, Lars ^b   Hanski, Ilkka ^a   Lehtonen, Rainer ^a   Auvinen, Petri ^b   Brudno, Michael ^c  

^a UNIVERSITY OF HELSINKI   (Finland)

^b UNIVERSITY OF HELSINKI   (Finland)

^c NONE

Author keywords

[No Author keywords available]

Indexed keywords

INSECT PROTEIN;

ANIMAL; ARTICLE; BIOLOGY; CHROMOSOME MAP; COMPUTER PROGRAM; FEMALE; GENETIC DATABASE; GENETIC LINKAGE; GENETICS; GENOME; HAPLOTYPE; LEPIDOPTERA; MEIOSIS; METHODOLOGY; SINGLE NUCLEOTIDE POLYMORPHISM;

ANIMALS; CHROMOSOME MAPPING; COMPUTATIONAL BIOLOGY; DATABASES, GENETIC; FEMALE; GENETIC LINKAGE; GENOME; HAPLOTYPES; INSECT PROTEINS; LEPIDOPTERA; LOD SCORE; MEIOSIS; POLYMORPHISM, SINGLE NUCLEOTIDE; SOFTWARE;

EID: 84898539524     PISSN: 13674803     EISSN: 14602059     Source Type: Journal    
DOI: 10.1093/bioinformatics/btt563     Document Type: Article

References (30)

1. Baxter, S. et al. (2011) Linkage mapping and comparative genomics using next-generation RAD sequencing of a non-model organism. PLoS One, 6, e19315.
2. Beldade, P. et al. (2009) A gene-based linkage map for Bicyclus anynana butterflies allows for a comprehensive analysis of synteny with the lepidopteran reference genome. PLoS Genet., 5, e1000366.
3. Broman, K. et al. (2003) R/qtl: QTL mapping in experimental crosses. Bioinformatics, 19, 889-890.
4. Cartwright, D. et al. (2007) Genetic mapping in the presence of genotyping errors. Genetics, 176, 2521-2527.
5. Cheema, J. and Dicks, J. (2009) Computational approaches and software tools for genetic linkage map estimation in plants. Brief. Bioinform., 10, 595-608.
6. de Givry, S. et al. (2005) Carthagene: multipopulation integrated genetic and radiation hybrid mapping. Bioinformatics, 21, 1703-1704.
7. Doerge, R. (2002) Mapping and analysis of quantitative trait loci in experimental populations. Nat. Rev. Genet., 3, 43-52.
8. Durbin, R. et al. (1998) Biological Sequence Analysis: Probabilistic Models of Proteins and Nucleic Acids. Cambridge University Press, Cambridge.
9. Ehrlich, P. and Hanski, I. (2004) On the Wings of Checkerspots: A Model System for Population Biology. Oxford University Press, New York.
10. Federley, H. (1938) Chromosomenzahlen finnlandischer Lepidopteren. I. Rhopalocera. Hereditas, XXIV, 397-464.
11. Garey, M. and Johnson, D. (1979) Computers and Intractability: A Guide to the Theory of NP-Completeness, W.H. Freeman & Co., NY, USA.
12. Hamming, R. (1950) Error detecting and error correcting codes. Bell Syst. Tech. J., 29, 147-160.
13. Iwata, H. and Ninomiya, S. (2006) Antmap: constructing genetic linkage maps using an ant colony optimization algorithm. Breed. Sci., 56, 371-377.
14. Jansen, J. et al. (2001) Constructing dense genetic linkage maps. Theor. Appl. Genet., 102, 1113-1122.
15. Kirkpatrick, S. et al. (1983) Optimization by simulated annealing. Science, 220, 671-680.
16. Laird, N. and Lange, C. (2008) Family-based methods for linkage and association analysis. In: Genetic Dissection of Complex Traits, Volume 60 of Advances in Genetics. Academic Press, pp. 219-252.
17. Lander, E. and Green, P. (1987) Construction of multilocus genetic linkage maps in humans. Proc. Natl Acad. Sci. USA, 84, 2363-2367.
18. Lathrop, G. et al. (1984) Strategies for multilocus linkage analysis in humans. Proc. Natl Acad. Sci. USA, 81, 3443-3446.
19. Li, H. and Durbin, R. (2009) Fast and accurate short read alignment with Burrows Wheeler transform. Bioinformatics, 25, 1754-1760.
20. Li, H. et al. (2009) The sequence alignment/map format and SAMtools. Bioinformatics, 25, 2078-2079.
21. Lincoln, S. and Lander, E. (1992) Systematic detection of errors in genetic linkage data. Genomics, 14, 604-610.
22. Miller, M. et al. (2007) Rapid and cost-effective polymorphism identification and genotyping using restriction site associated DNA (RAD) markers. Genome Res., 17, 240-248.
23. Morton, N. (1955) Sequential tests for the detection of linkage. Am. J. Hum. Gen., 7, 277-318.
24. Stam, P. (1993) Construction of integrated genetic linkage maps by means of a new computer package: join map. Plant J., 3, 739-744.
25. Van Ooijen, J. (2011) Multipoint maximum likelihood mapping in a full-sib family of an outbreeding species. Genet. Res., 93, 343-349.
26. van Os, H. et al. (2005a) Record: a novel method for ordering loci on a genetic linkage map. Theor. Appl. Genet., 112, 30-40.
27. van Os, H. et al. (2005b) Smooth: a statistical method for successful removal of genotyping errors from high-density genetic linkage data. Theor. Appl. Genet., 112, 187-194.
28. Wu, Y. et al. (2008) Efficient and accurate construction of genetic linkage maps from the minimum spanning tree of a graph. PLoS Genet., 4, e1000212.
29. Yamamoto, K. et al. (2006) Construction of a single nucleotide polymorphism linkage map for the silkworm, Bombyx mori, based on bacterial artificial chromosome end sequences. Genetics, 173, 151-161.
30. Yasukochi, Y. (1998) A dense genetic map of the silkworm, Bombyx mori, covering all chromosomes based on 1018 molecular markers. Genetics, 150, 1513-1525.