Algorithms to distinguish the role of gene-conversion from single-crossover recombination in the derivation of SNP sequences in populations

Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)

Volumn 3909 LNBI, Issue , 2006, Pages 231-245

  Song, Yun S ^a   Ding, Zhihong ^a   Gusfield, Dan ^a   Langley, Charles H ^b   Wu, Yufeng ^a  

^a University of California   (United States)

^b UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ALGORITHMS; BIODIVERSITY; BOUNDARY CONDITIONS; COMPUTATION THEORY; COMPUTER SIMULATION; DNA SEQUENCES; GENES; LINEAR PROGRAMMING; MUTAGENESIS;

CROSSING-OVER; GENE-CONVERSION; MEIOTIC RECOMBINATION; SNP SEQUENCES;

MOLECULAR BIOLOGY;

EID: 33745777779     PISSN: 03029743     EISSN: 16113349     Source Type: Book Series    
DOI: 10.1007/11732990_20     Document Type: Conference Paper

References (30)

1. V. Bafna and V. Bansal. The number of recombination events in a sample history: conflict graph and lower bounds. IEEE/ACM Transactions on Computational Biology and Bioinformatics, 1:78-90, 2004.
2. V. Bafna and V. Bansal. Improved recombination lower bounds for haplotype data. In Proceedings of RECOMB 2005, pages 569-584, 2005.
3. C. Carlson, M. Eberle, L. Kruglyak, and D. Nickerson. Mapping complex disease loci in whole-genome association studies. Nature, 429:446-452, 2004.
4. A. G. Clark. Finding genes underlying risk of complex disease by linkage disequilibrium mapping. Cure. Opin. Genet. Dev., 13:296-302, 2003.
5. G. Drouin, F. Prat, M. Ell, and G.D. Clarke. Detecting and characterizing gene conversion between multigene family members. Mol. Bio. Evol., 16:1369-1390, 1999.
6. N. El-Mabrouk. Deriving haplotypes through recombination and gene conversion pathways. J. Bioinformatics and Computational Biology, 2(2):241-256, 2004.
7. P. Fearnhead, R.M. Harding, J.A. Schneider, S. Myers, and P. Donnelly. Application of coalescent methods to reveal fine scale rate variation and recombination hotspots. Genetics, 167:2067-2081, 2004.
8. L. Frisse, R.R. Hudson, A. Bartoszewicz, J.D. Wall, J. Donfack, and A. Di Rienzo. Gene conversion and different population histories may explain the contrast between polymorphism and linkage disequilibrium levels. Am. J. Hum. Genet., 69:831-843, 2001.
9. D. Gusfield. Optimal, efficient reconstruction of Root-Unknown phylogenetic networks with constrained and structured recombination. JCSS, 70:381-398, 2005.
10. D. Gusfield, S. Eddhu, and C. Langley. The fine structure of galls in phylogenetic networks. INFORMS J. on Computing, special issue on Computational Biology, 16:459-469, 2004.
11. D. Gusfield, S. Eddhu, and C. Langley. Optimal, efficient reconstruction of phylo genetic networks with constrained recombination. J. Bioinformatics and Computational Biology, 2(1):173-213, 2004.
12. D. Gusfield, D. Hickerson, and S. Eddhu. An efficiently-computed lower bound on the number of recombinations in phylogenetic networks: Theory and empirical study. To appear in Discrete Applied Math, special issue on Computational Biology.
13. J. Hein. Reconstructing evolution of sequences subject to recombination using parsimony. Math. Biosci, 98:185-200, 1990.
14. J. Hein. A heuristic method to reconstruct the history of sequences subject to recombination. J. Mol. Evol., 36:396-405, 1993.
15. J. Hein, M. Schierup, and C. Wiuf. Gene Genealogies, Variation and Evolution: A primer in coalescent theory. Oxford University Press, UK, 2004.
16. R. Hudson. Generating samples under the Wright-Fisher neutral model of genetic variation. Bioinformatics, 18(2):337-338, 2002.
17. R. Hudson and N. Kaplan. Statistical properties of the number of recombination events in the history of a sample of DNA sequences. Genetics, 111:147-164, 1985.
18. A. J. Jeffreys and C. A. May. Intense and highly localized gene conversion activity in human meiotic crossover hot spots. Nature Genetics, 36:151-156, 2004.
19. M. Lajoie and N. El-Mabrouk. Recovering haplotype structure through recombination and gene conversion. Bioinformatics, 21(Suppl 2):ii173-ii179, 2005.
20. S. R. Myers and R. C. Griffiths. Bounds on the minimum number of recombination events in a sample history. Genetics, 163:375-394, 2003.
21. B. Padhukasahasram, P. Marjoram, and M. Nordborg. Estimating the rate of gene conversion on human chromosome 21. Am. J. Hum. Genet., 75:386-97, 2004.
22. V. Plagnol, B. Padhukasahasram, J. D. Wall, P. Marjoram, and M. Nordborg. Relative influences of crossing-over and gene conversion on the pattern of linkage disequilibrium in Arabidopsis thaliana. Genetics, in press. Ahead of Print: 10.1534/genetics.l04.040311.
23. S. Sawyer. Statistical tests for detecting gene conversion. Mol. Biol. Evol., 6:526-538, 1989.
24. Y.S. Song and J. Hein. Parsimonious reconstruction of sequence evolution and haplotype blocks: Finding the minimum number of recombination events. In Proc. of 2003 Workshop on Algorithms in Bioinformatics, pages 287-302, 2003.
25. Y.S. Song and J. Hein. On the minimum number of recombination events in the evolutionary history of DNA sequences. J. Math. Biol., 48:160-186, 2004.
26. Y.S. Song, Y. Wu, and D. Gusfield. Efficient computation of close lower and upper bounds on the minimum number of needed recombinations in the evolution of biological sequences. Proc. of ISMB 2005, Bioinformatics, 21:i413-i422, 2005.
27. J. C. Stephens. Statistical methods of DNA sequence analysis: Detection of intragenic recombination or gene conversion. Mol. Bio. Evol., 2:539-556, 1985.
28. The International HapMap Consortium. A haplotype map of the human genome. Nature, 437:1299-1320, 2005.
29. J. D. Wall. Close look at gene conversion hot spots. Nat. Genet., 36:114-115, 2004.
30. T. Wiehe, J. Mountain, P. Parham, and M. Slatkin. Distinguishing recombination and intragenic gene conversion by linkage disequilibrium patterns. Genet. Res., Camb., 75:61-73, 2000.