Modified SIMPSON O(n3) algorithm for the full sibship reconstruction problem

Bioinformatics

Volumn 21, Issue 20, 2005, Pages 3912-3917

  Konovalov, Dmitry A ^a   Bajema, Nigel ^a   Litow, Bruce ^a  

^a JAMES COOK UNIVERSITY   (Australia)

Author keywords

[No Author keywords available]

Indexed keywords

DNA MARKER;

ACCURACY; ARTICLE; CLUSTER ANALYSIS; CONTROLLED STUDY; DIPLOIDY; FAMILY SIZE; GENETIC ALGORITHM; GENETIC DISTANCE; GENOTYPE; HUMAN; INTERMETHOD COMPARISON; MATHEMATICAL COMPUTING; POPULATION GENETICS; PRIORITY JOURNAL; SIBLING; SIMULATION; TIME;

EID: 27544494125     PISSN: 13674803     EISSN: 13674811     Source Type: Journal    
DOI: 10.1093/bioinformatics/bti642     Document Type: Article

References (17)

1. Abramowitz,M. and Stegun,I.A. (1972) Handbook of Mathematical Functions with Formulas, Graphs, and Mathematical Tables. 9th printing edn. Dover, New York.
2. Almudevar,A. (2001) A bootstrap assessment of variability in pedigree reconstruction based on genetic markers. Biometrics, 57, 757-763.
3. Almudevar,A. and Field,C. (1999) Estimation of single-generation sibling relationships based on DNA markers. J. Agri. Biol. Environ. Stat., 4, 136-165.
4. Bell,E.T. (1934) Exponential numbers. Amer. Math. Monthly, 41, 411-419.
5. Beyer,J. and May,B. (2003) A graph-theoretic approach to the partition of individuals into full-sib families. Mol. Ecol., 12, 2243-2250.
6. Blouin,M.S. (2003) DNA-based methods for pedigree reconstruction and kinship analysis in natural populations. Trends Ecol. Evol., 18, 503-511.
7. Blouin,M.S. et al. (1996) Use of microsatellite loci to classify individuals by relatedness. Mol. Ecol., 5, 393-401.
8. Butler,K. et al. (2004) Accuracy, efficiency and robustness of four algorithms allowing full sibship reconstruction from DNA marker data. Mol. Ecol., 13, 1589-1600.
9. Gusfield,D. (2002) Partition-distance: A problem and class of perfect graphs arising in clustering. Inform. Proc. Lett., 82, 159-164.
10. Konovalov,D.A. et al. (2005) Partition-distance via the assignment problem. Bioinformatics, 21, 2463-2468.
11. Konovalov,D.A. et al. (2004) KinGroup: A program for pedigree relationship reconstruction and kin group assignments using genetic markers. Mol. Ecol. Notes, 4, 779-782.
12. Lovasz,L. (1993) Combinatorial Problems and Exercises. 2nd edn. Netherlands: North-Holland, Amsterdam.
13. Pemberton,J. (2004) Measuring inbreeding depression in the wild: The old ways are the best. Trends Ecol. Evol., 19, 613-615.
14. Smith,B.R. et al. (2001) Accurate partition of individuals into full-sib families from genetic data without parental information. Genetics, 158, 1329-1338.
15. Thomas,S.C. and Hill,W.G. (2000) Estimating quantitative genetic parameters using sibships reconstructed from marker data. Genetics, 155, 1961-1972.
16. Thomas,S.C. and Hill,W.G. (2002) Sibship reconstruction in hierarchical population structures using Markov chain Monte Carlo techniques. Genet. Res., 79, 227-234.
17. Wang,J.L. (2004) Sibship reconstruction from genetic data with typing errors. Genetics, 166, 1963-1979.