The task of haplotype block partitioning and “tag SNPs” selection requires large sets of genotype data for each of the populations studied. Even though the availability of datasets and tools is increasing with the advent of the International HapMap Project and other SNP databases, characterizing the haplotype structures of genes is still a laborious task. For example, datasets need to be downloaded from public databases and organized into required formats before being fed to haplotyping tools. The results obtained from the tools often require further conversions for analysis and display.

HapBlock, a suite of dynamic programming algorithms and logical rules developed by Zhang et al [1], is able to perform block partitioning and tag SNP selection for genotype or haplotype data from both unrelated individuals and general pedigrees using different haplotype block and tag SNP definitions.

We have built a pipeline which incorporates the functionalities of HapBlock to analyze HapMap data (HapMap Public Release #21, Jul 2006). The pipeline automates the characterization of haplotype block structures of genes by providing a user-friendly web-based interface. Users can supply a gene name and the pipeline returns a list of identified genes and their chromosomal locations. Regions upstream and downstream of the selected gene and other parameter values involving haplotype block and tag SNPs definitions will be subsequently required from the user. The pipeline then retrieves the genotype data from HapMap, filters out the irrelevant data and invokes HapBlock to identify the haplotype blocks and tag SNPs. The textual output from HapBlock is then converted to dynamically generated graphics that depict the haplotype blocks. The results obtained are finally displayed as hypertext markup language (HTML) files which can be visualized using standard web-browsers.

View the iHAP poster presented at PSB 2006.

[1] Zhang K, Qin Z, Chen T, Liu JS, Waterman MS, Sun F. HapBlock: haplotype block partitioning and tag SNP selection software using a set of dynamic programming algorithms. Bioinformatics. 21(1):131-4 (2005).

[2] Daly MJ, Rioux JD, Schaffner SF, Hudson TJ, Lander ES. High-resolution haplotype structure in the human genome. Nat Genet. 29(2):229-32 (2001).

 
 
 
iHAP was developed by:

Song Chun Meng, Alfred, Yeo Boon Huat, Benjamin, Tantoso Erwin and Yang Yuchen

Acknowledgements:

Web Services Team:
Danny Chuon
Hazel Chua

For more information, email us at ihap@bii.a-star.edu.sg