ViewGene: a Graphical Tool for SNP Visualization and Characterization
The Human Genome Project has produced an enormous amount of sequence data, based on which single base changes between individuals are being identified. Unfortunately, computer tools that were adequate for sequence assembly are less than ideal for the characterization of single nucleotide polymorphism (SNP) data and its relationship to established sequence features. JHU researchers 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 scafflod that can be viewed through a simple graphical interface. SNPs generated from many sources can be added to this scaffold, with a variety of options to control what is displayed. Large amounts of SNP data can be organized so that patterns and haplotypes can be readily discerned. In the laboratory, ViewGene has been used to view annotated Genebank records, find nonrepetitive sequence fragments for SNP detection, and visualize similarity search results. Description (Set) viewGene is written in the Java programming language, which is well suited for a graphical application in our multiplatform environment. The code has been tested on Microsoft Windows, Sun Solaris, Linux, and Macintosh (OS X) computers and should run on any operating system that has access to a Java 1.2 virtual machine. viewGene was developed in the Java 1.2 programming language, using Metrowerks CodeWarrior and Sun Microsystems development tools. The distribution will contain a Java class archive sufficient to run viewGene in any environment that supports the Java 1.2 language, as well as the sample data set used to create the accompanying figures and other examples of assembly files and scripts for parsing common data types. Currently supported file formats are GenBank, Sim4, and Genscan genes; RepeatMasker and Miropeats similarity analysis data; FASTA, BLAST, and Cross match sequence data. Proposed Use (Set) Software research tool may be used for the manipulation, cross-referencing and haplotype analysis of SNP data are essential for SNP quality assessment and identification of SNPs associated with genetic disease.Inventor(s): Kashuk, Carl S.
Type of Offer: Licensing
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