HapScope

A software system for automated and visual analysis of functionally annotated haplotypes

Jinghui Zhang, William L. Rowe, Jeffrey P. Struewing, Kenneth Buetow

Research output: Contribution to journalArticle

28 Citations (Scopus)

Abstract

We have developed a software analysis package, HapScope, which includes a comprehensive analysis pipeline and a sophisticated visualization tool for analyzing functionally annotated haplotypes. The HapScope analysis pipeline supports: (i) computational haplotype construction with an expectation-maximization or Bayesian statistical algorithm; (ii) SNP classification by protein coding change, homology to model organisms or putative regulatory regions; and (iii) minimum SNP subset selection by either a Brute Force Algorithm or a Greedy Partition Algorithm. The HapScope viewer displays genomic structure with haplotype information in an integrated environment, providing eight alternative views for assessing genetic and functional correlation. It has a user-friendly interface for: (i) haplotype block visualization; (ii) SNP subset selection; (iii) haplotype consolidation with subset SNP markers; (iv) incorporation of both experimentally determined haplotypes and computational results; and (v) data export for additional analysis. Comparison of haplotypes constructed by the statistical algorithms with those determined experimentally shows variation in haplotype prediction accuracies in genomic regions with different levels of nucleotide diversity. We have applied HapScope in analyzing haplotypes for candidate genes and genomic regions with extensive SNP and genotype data. We envision that the systematic approach of integrating functional genomic analysis with population haplotypes, supported by HapScope, will greatly facilitate current genetic disease research.

Original languageEnglish (US)
Pages (from-to)5213-5221
Number of pages9
JournalNucleic Acids Research
Volume30
Issue number23
DOIs
StatePublished - Dec 1 2002
Externally publishedYes

Fingerprint

Haplotypes
Software
Single Nucleotide Polymorphism
Genetic Research
Inborn Genetic Diseases
Nucleic Acid Regulatory Sequences
Nucleotides
Genotype

ASJC Scopus subject areas

  • Genetics

Cite this

HapScope : A software system for automated and visual analysis of functionally annotated haplotypes. / Zhang, Jinghui; Rowe, William L.; Struewing, Jeffrey P.; Buetow, Kenneth.

In: Nucleic Acids Research, Vol. 30, No. 23, 01.12.2002, p. 5213-5221.

Research output: Contribution to journalArticle

Zhang, Jinghui ; Rowe, William L. ; Struewing, Jeffrey P. ; Buetow, Kenneth. / HapScope : A software system for automated and visual analysis of functionally annotated haplotypes. In: Nucleic Acids Research. 2002 ; Vol. 30, No. 23. pp. 5213-5221.
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