Abstract Background: Haplotypes are important for assessing genealogy and disease susceptibility of individual genomes, but are difficult to obtain with routine sequencing approaches. Experimental haplotype reconstruction based on assembling fragments of individual chromosomes is promising

, but with variable yields due to incompletely understood parameter choices. Results: We parameterize the clone-based haplotyping problem in order to provide theoretical and empirical assessments of the impact of different parameters on haplotype assembly. We confirm the intuition that long clones help link together

This Provisional PDF corresponds to the article as it appeared upon acceptance. Copyedited and fully formatted PDF and full text (HTML) versions will be made available soon. On the design of clone-based haplotyping

of large-insert clones, such that the assembly corresponding to each clone represents a single haplotype 9 . One of the first 'personal genomes' exploited clone-based mate pairing and long, accurate Sanger reads to resolve variants into haplotype blocks (N50 of 350 kbp; that is, 50% of resolved

set of 14 haplotype-resolved genomes generated by fosmid clone-based sequencing, complemented and expanded by up to 372 statistically resolved genomes from the 1000 Genomes Project. We find immense diversity of both haploid and diploid gene forms, up to 4.1 and 3.9 million corresponding to 249 and 235

constructed into a multivariate mixture model for genetic mapping. This integrative mapping model on the foundation of linkage disequilibrium (LD)-based haplotype block analysis provides unique power to precisely detect human quantitative trait loci (QTL) determining HIV-1 dynamics and facilitates positional

-pollination of stigmas at various stages of development was performed as described in Figure 2. A self-incompatible and a PSC plant were included as controls. Arrows indicate the breakdown of SI in the PSC plant starting at stage +2 stigmas. Based on these initial pollination results and the extent of seed set observed

haplotypes derived from 26 polymorphisms in the promoter, 59UTR, coding, and 39UTR of the intronless ADRB2 gene. These were cloned into an expression construct lacking a vector-based promoter, so that b2AR expression was driven by its promoter, and steady state expression could be modified by polymorphisms

of such haplotypes by the new model will facilitate the molecular cloning of a QTL. Our model is founded on population genetic properties of genes that are segregating in a pedigree, constructed with the mixture-based maximum likelihood context and implemented with the EM algorithm. The closed forms have been

. The effect of PCR amplification was analysed. Error correction resulted in a two- and five-fold decrease of the pyrosequencing base substitution rate, from 0.05 % to 0.03 % and from 0.25 % to 0.05 % in the non-PCR and PCR-amplified samples, respectively. We were able to detect viral clones as rare as 0