Global haplotype partitioning for maximal associated SNP pairs

BMC Bioinformatics

Table 1 Summary of haplotype block partitioning methods compared in this study.

abbr.	Method	Partitioning structure	Block definition	Block constraint	Software	Ref.
HOT	Hotspot	Local*	recombination hotspots	none	"precomputed results available by HapMap"	[4]
MB	Minimum block number	Global	minimum number of blocks	haplotype diversity	HapBlock v.3	[23]
HB	HapBlock	Global	minimizing total number of tagSNPs	haplotype diversity	HapBlock v.3	[23]
MDL	MDBlock	Global	minimum description length	haplotype diversity	MDBlock v.1	[43]
GAM	Four gamete test	Local	evidence of recombination	fourth gamete	Haploview v.4	[44]
GAB	Gabriel's method	Local	evidence of recombination	strongly associated SNPs	Haploview v.4	[26]
GPG	GPMAP** based on Gabriel's index	Global	maximizing associated SNPs	independent SNPs	Haploview+GPMAP	present paper
GPF	GPMAP based on Fisher's exact Test	Global	maximizing associated SNPs	independent SNPs	Haploview+GPMAP	present paper

* The approach of the original method is recognized as a local partitioning. ** Global Partitioning for Maximal Association Pairs

ISSN: 1471-2105