title: iHAP--integrated haplotype analysis pipeline for characterizing the haplotype structure of genes.
abstract: BACKGROUND
  The advent of genotype data from large-scale efforts that catalog the genetic variants of different populations have given rise to new avenues for multifactorial disease association studies. Recent work shows that genotype data from the International HapMap Project have a high degree of transferability to the wider population. This implies that the design of genotyping studies on local populations may be facilitated through inferences drawn from information contained in HapMap populations.
  
  
  RESULTS
  To facilitate analysis of HapMap data for characterizing the haplotype structure of genes or any chromosomal regions, we have developed an integrated web-based resource, iHAP. In addition to incorporating genotype and haplotype data from the International HapMap Project and gene information from the UCSC Genome Browser Database, iHAP also provides capabilities for inferring haplotype blocks and selecting tag SNPs that are representative of haplotype patterns. These include block partitioning algorithms, block definitions, tag SNP definitions, as well as SNPs to be "force included" as tags. Based on the parameters defined at the input stage, iHAP performs on-the-fly analysis and displays the result graphically as a webpage. To facilitate analysis, intermediate and final result files can be downloaded.
  
  
  CONCLUSIONS
  The iHAP resource, available at http://ihap.bii.a-star.edu.sg, provides a convenient yet flexible approach for the user community to analyze HapMap data and identify candidate targets for genotyping studies.
authors.affiliation: Bioinformatics Institute, 30 Biopolis Street, #07-01, 138671, Singapore. alfreds@bii.a-star.edu.sg <alfreds@bii.a-star.edu.sg>
authors.forename: Chun Meng
authors.initials: CM
authors.lastname: Song
authors.forename: Boon Huat
authors.initials: BH
authors.lastname: Yeo
authors.forename: Erwin
authors.initials: E
authors.lastname: Tantoso
authors.forename: Yuchen
authors.initials: Y
authors.lastname: Yang
authors.forename: Yun Ping
authors.initials: YP
authors.lastname: Lim
authors.forename: Kuo-Bin
authors.initials: KB
authors.lastname: Li
authors.forename: Gunaretnam
authors.initials: G
authors.lastname: Rajagopal
mesh_terms: D000465:Algorithms; D001483:Base Sequence; D002874:Chromosome Mapping / Q000379:methods*; D030541:Databases, Genetic; D014644:Genetic Variation / Q000235:genetics; D006239:Haplotypes / Q000235:genetics*; D016247:Information Storage and Retrieval / Q000379:methods*; D008969:Molecular Sequence Data; D017422:Sequence Analysis, DNA / Q000379:methods*; D012984:Software