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ViewGene: a graphical tool for polymorphism visualization and characterization.

Carl Kashuk1, Sanghamitra SenGupta, Evan Eichler

  • 1McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland 21287, USA.

Genome Research
|February 6, 2002
PubMed
Summary
This summary is machine-generated.

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viewGene is a flexible tool for analyzing human genome sequence data, including single nucleotide polymorphisms (SNPs) and insertion/deletions (indels). It helps organize and visualize polymorphism data to identify disease-associated variants.

Area of Science:

  • Genomics
  • Bioinformatics

Background:

  • The Human Genome Project generates vast amounts of sequence data.
  • Existing computational tools are inadequate for characterizing complex polymorphism data and its relationships.

Purpose of the Study:

  • To develop a flexible tool, viewGene, for visualizing and analyzing sequence data and polymorphisms.
  • To facilitate the organization and discernment of patterns and haplotypes within large polymorphism datasets.

Main Methods:

  • viewGene accepts input from various sequence formats and analysis programs (Genbank, FASTA, RepeatMasker, Cross match, BLAST).
  • It constructs a sequence reference scaffold with options to display polymorphisms from multiple sources.
  • The tool supports manipulation, cross-referencing, and haplotype viewing of SNP data.

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Main Results:

  • viewGene has been successfully used to view annotated Genbank records and similarity search results.
  • It aids in identifying nonrepetitive sequence fragments for polymorphism detection.
  • The tool effectively organizes and visualizes large amounts of polymorphism data, enabling pattern and haplotype discernment.

Conclusions:

  • viewGene provides essential functions for quality assessment and identification of variants associated with genetic disease.
  • It offers a flexible and user-friendly graphical interface for complex genomic data analysis.