viewGene: A graphical tool for polymorphism visualization and characterization

Carl Kashuk, Sanghamitra Sengupta, Evan Eichler, Aravinda Chakravarti

Research output: Contribution to journalArticlepeer-review

Abstract

The human genome project is producing an enormous amount of sequence data, based on which single base changes between individuals can be identified. Unfortunately, computer tools that were adequate for sequence assembly are less than ideal for the characterization of polymorphism data [single nucleotide (snp) or insertion/deletion (indel)] and other sequence features, and their relationship to each other. We have developed viewGene as a flexible tool that takes input from a number of sequence formats and analysis programs (Genbank, FASTA, RepeatMasker, Cross match, BLAST, user-defined data) to construct a sequence reference scaffold that can be viewed through a simple graphical interface. polymorphisms generated from many sources can be added to this scaffold through the same sequence formats, with a variety of options to control what is displayed. Large amounts of polymorphism data can be organized so that patterns and haplotypes can be readily discerned. in our laboratory, viewGene has been used to view annotated genbank records, find nonrepetitive sequence fragments for polymorphism detection, and visualize similarity search results. Manipulation, cross-referencing, and haplotype viewing of snp data are essential for quality assessment and identification of variants associated with genetic disease, and viewGene provides all three of these important functions.

Original languageEnglish (US)
Pages (from-to)333-338
Number of pages6
JournalGenome research
Volume12
Issue number2
DOIs
StatePublished - 2002

ASJC Scopus subject areas

  • Genetics
  • Genetics(clinical)

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