SNP-VISTA

Software · Mon Nov 07 00:00:00 EST 2005

DOI:https://doi.org/10.11578/dc.20220414.67· OSTI ID:1247304 · Code ID:73223

Shah, Nameeta; Teplitsky, Michael; Minovitsky, Simon; Dubchak, Inna

SNP-VISTA aids in analyses of the following types of data: A. Large-scale re-sequence data of disease-related genes for discovery of associated and/or causative alleles (GeneSNP-VISTA). B. Massive amounts of ecogenomics data for studying homologous recombination in microbial populations (EcoSNP-VISTA). The main features and capabilities of SNP-VISTA are: 1) Mapping of SNPs to gene structure; 2) classification of SNPs, based on their location in the gene, frequency of occurrence in samples and allele composition; 3) clustering, based on user-defined subsets of SNPs, highlighting haplotypes as well as recombinant sequences; 4) integration of protein conservation visualization; and 5) display of automatically calculated recombination points that are user-editable. The main strength of SNP-VISTA is its graphical interface and use of visual representations, which support interactive exploration and hence better understanding of large-scale SNPs data.

• Short Name / Acronym: SNP-VISTA
• Project Type: Open Source, No Publicly Available Repository
• Site Accession Number: 3844
• Software Type: Scientific
• License(s): Other
• Programming Language(s): GNU C++compiler
• Research Organization: Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)
• Sponsoring Organization: USDOE

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  Primary Award/Contract Number:

  AC02-05CH11231
• DOE Contract Number: AC02-05CH11231
• Code ID: 73223
• OSTI ID: 1247304
• Country of Origin: United States