Simulating haplotype blocks in the human genome.
CONCLUSIONS
A bioinformatic tool was written to simulate haplotypes and SNPs under a modified coalescent with recombination. The most important feature of this program is that it allows for the specification of non-homogeneous recombination rates, which results in the formation of the so-called 'haplotype blocks' of the human genome. The program also implements different mutation models and flexible demographic histories. The samples generated can be very useful to better understand the architecture of the human genome and to investigate its impact in association studies searching for disease genes.


BACKGROUND
The SNPsim package is available at http://www.evolgenics.com/software
Posada
David
D
Variagenics Inc., 60 Hampshire St, Cambridge, MA 02139-1548, USA. dposada@evolgenics.com
Wiuf
Carsten
C
D000465:Algorithms; D001483:Base Sequence; D003198:Computer Simulation; D030541:Databases, Genetic; D005787:Gene Frequency / Q000235:genetics; D015894:Genome, Human; D006239:Haplotypes; D006801:Humans; D015810:Linkage Disequilibrium / Q000235:genetics; D008957:Models, Genetic; D008969:Molecular Sequence Data; D020641:Polymorphism, Single Nucleotide; D011786:Quality Control; D011995:Recombination, Genetic / Q000235:genetics; D012689:Sequence Homology, Nucleic Acid; D014584:User-Computer Interface