RT Journal
A1 Kashuk, Carl
A1 SenGupta, Sanghamitra
A1 Eichler, Evan
A1 Chakravarti, Aravinda
T1 

viewGene
: A Graphical Tool for Polymorphism Visualization and Characterization
JF Genome Research 
JO Genome Research 
YR 2002 
FD February 01 
VO 12 
IS 2 
SP 333 
OP 338 
DO 10.1101/gr.211202 
UL http://genome.cshlp.org/content/12/2/333.abstract 
AB 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 viewGeneas 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.