Efficient Haplotype Block Partitioning and Tag SNP Selection Algorithms under Various Constraints

Table 1

Comparison of properties of haplotype blocks defined by Zhang, Patil, and us with 80% of common haplotype coverage, using the chromosome 21 haplotype sample proposed by Patil.

Method	Common SNPs per block	No. of blocks	No. of blocks requiring ≥1 tagSNPs	Average no. of common haplotype per block	Block frequency (%)	SNP frequency (%)
HBPTS	>10	736	733	4.32	32.5	77.8
	3–10	751	686	3.16	33.1	18.0
	<3	779	216	2.12	34.4	4.2
	Total	2,266	1,635	3.18	100.0	100.00
Zhang’s	>10	742	738	4.23	28.8	75.5
	3–10	909	842	3.03	35.3	19.5
	<3	924	274	2.12	35.9	5.0
	Total	2,575	1,854	3.05	100.0	100.0
Patil’s	>10	589	589	3.75	14.2	56.8
	3–10	1,408	1,396	2.92	34.1	30.7
	<3	2,138	1,776	2.30	51.7	12.4
	Total	4,135	3,761	2.72	100.0	100.0