viewGene: A Graphical Tool for Polymorphism Visualization and Characterization

摘要: 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 assembly are less than ideal the characterization polymorphism data [single nucleotide (snp) or insertion/deletion (indel)] and other features, their relationship to each other. We have developed viewGene as a flexible tool takes input from number formats analysis programs (Genbank, FASTA, RepeatMasker, Cross match, BLAST, user-defined data) construct reference scaffold viewed through simple graphical interface. polymorphisms generated many sources added this same formats, with variety options control what displayed. Large amounts organized so patterns haplotypes readily discerned. in our laboratory, has been used view annotated genbank records, find nonrepetitive fragments detection, visualize similarity search results. Manipulation, cross-referencing, haplotype viewing snp essential quality assessment identification variants associated genetic disease, provides all three these important functions. Several genomic viewers now available assemblies sequence, including annotation genes, repeats, polymorphisms, features. Human Genome Project Working Draft (http://genome.ucsc. edu), Ensembl (http://www.ensembl.org), NCBI Map Viewer (http://www.ncbi.nlm.nih.gov) provide interpretations at chromosome level. These sites useful feature interest, if it exists public record, how relates contigs, radiation hybrid maps. useful, however, characterize collection features newly discovered laboratory. functionality viewer “local level” (generally under megabase sequence; current code handle larger sequences but suboptimal performance). User relation results standard software, taken above custom annotation. Data combined displayed common coordinate system further analysis. being laboratory assist